Experiment: 2PE5

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EFA	PDB entry 1EFA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	281	1.8 M Ammonium Sulfate, 0.1 M Hepes pH 7.5. 11% PEG 400, 14% glycerol, 10X ONPG, VAPOR DIFFUSION, HANGING DROP, temperature 281K

Crystal Properties
Matthews coefficient	Solvent content
5.03	75.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 253.08	α = 90
b = 253.08	β = 90
c = 203.247	γ = 120

Symmetry
Space Group	H 3 2

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	Osmic mirrors	2006-03-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	3.5	20	99.89	0.176	0.176	7.3	9.1	31342	29717	-3	-3	25.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	3.5	3.6	99.7		0.504	0.504	4.37	6.9	2090

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 1EFA	3.5	19.98	29717	29717	1581	99.86	0.23616	0.23616	0.23347	0.28656	RANDOM	53.844

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]
-0.02	-0.01		-0.02		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.867
r_dihedral_angle_3_deg	20.917
r_dihedral_angle_4_deg	17.201
r_dihedral_angle_1_deg	5.896
r_scangle_it	1.752
r_angle_refined_deg	1.627
r_mcangle_it	0.983
r_scbond_it	0.927
r_mcbond_it	0.551
r_nbtor_refined	0.308

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.867
r_dihedral_angle_3_deg	20.917
r_dihedral_angle_4_deg	17.201
r_dihedral_angle_1_deg	5.896
r_scangle_it	1.752
r_angle_refined_deg	1.627
r_mcangle_it	0.983
r_scbond_it	0.927
r_mcbond_it	0.551
r_nbtor_refined	0.308
r_nbd_refined	0.224
r_chiral_restr	0.145
r_symmetry_vdw_refined	0.144
r_xyhbond_nbd_refined	0.143
r_symmetry_hbond_refined	0.108
r_bond_refined_d	0.009
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7418
Nucleic Acid Atoms	1046
Solvent Atoms
Heterogen Atoms	63

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
DENZO	data reduction
SCALEPACK	data scaling
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.