Experiment: 1YQ2

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DP0	PDB ENTRY 1DP0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	291	PEG 4000, sodium chloride, amonium sulphate, sodium citrate buffer, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.62	68.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 140.091	α = 90
b = 205.698	β = 102.34
c = 140.458	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	CCD	ADSC QUANTUM 210		2003-09-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.9168	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.9	40	95	0.085	10.3	2.6	607777	577572		-5	17

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.9	1.93	81		0.451	2.1	1.9	24388

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 1DP0	1.9	40	607830	577466	5775	95.02	0.15702	0.15702	0.15701	0.195	RANDOM	18.018

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]
-0.16		-0.35	0.64		-0.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.663
r_dihedral_angle_4_deg	17.565
r_dihedral_angle_3_deg	13.463
r_dihedral_angle_1_deg	6.298
r_scangle_it	3.514
r_scbond_it	2.206
r_angle_refined_deg	1.472
r_mcangle_it	1.399
r_mcbond_it	0.78
r_nbtor_refined	0.307

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.663
r_dihedral_angle_4_deg	17.565
r_dihedral_angle_3_deg	13.463
r_dihedral_angle_1_deg	6.298
r_scangle_it	3.514
r_scbond_it	2.206
r_angle_refined_deg	1.472
r_mcangle_it	1.399
r_mcbond_it	0.78
r_nbtor_refined	0.307
r_symmetry_hbond_refined	0.228
r_nbd_refined	0.193
r_symmetry_vdw_refined	0.151
r_xyhbond_nbd_refined	0.141
r_metal_ion_refined	0.116
r_chiral_restr	0.105
r_bond_refined_d	0.013
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	47305
Nucleic Acid Atoms
Solvent Atoms	6513
Heterogen Atoms	79

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement

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.