Experiment: 3H9G

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3H5A	PDB entry 3H5A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	291.2	24-26% Pentaerythritol ethoxylate (15/4 EO/OH, Hampton Research), 50 mM Tris-HCl pH 8.0, 50 mM (NH4)2SO4, 10 mM MccA-N7isoAsn, VAPOR DIFFUSION, HANGING DROP, temperature 291.2K

Crystal Properties
Matthews coefficient	Solvent content
1.94	36.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.929	α = 90
b = 138.217	β = 92.38
c = 80.799	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 300 mm plate	Rosenbaum-Rock vertical focusing mirror	2007-12-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.97926	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.2	50	96.7	0.065	21.914	4.1	60798	60798			33.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.28	90.5		0.371		3.6	5645

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3H5A	2.2	46.88	62124	60091	3041	96.73	0.206	0.203	0.203	0.261	RANDOM	36.297

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
0.44		-0.03	-1.05		0.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.142
r_dihedral_angle_4_deg	17.641
r_dihedral_angle_3_deg	15.297
r_dihedral_angle_1_deg	5.28
r_scangle_it	2.217
r_scbond_it	1.591
r_mcangle_it	1.116
r_angle_refined_deg	1.103
r_mcbond_it	0.794
r_nbtor_refined	0.303

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.142
r_dihedral_angle_4_deg	17.641
r_dihedral_angle_3_deg	15.297
r_dihedral_angle_1_deg	5.28
r_scangle_it	2.217
r_scbond_it	1.591
r_mcangle_it	1.116
r_angle_refined_deg	1.103
r_mcbond_it	0.794
r_nbtor_refined	0.303
r_nbd_refined	0.201
r_symmetry_vdw_refined	0.195
r_xyhbond_nbd_refined	0.146
r_symmetry_hbond_refined	0.131
r_chiral_restr	0.075
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10767
Nucleic Acid Atoms
Solvent Atoms	511
Heterogen Atoms	39

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
X-GEN	data scaling
HKL-2000	data reduction
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.