Experiment: 2GRY

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	291	3.5M sodium formate, 0.1M sodium acetate, pH 4.6, vapor diffusion, sitting drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.3	62.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.475	α = 90
b = 121.475	β = 90
c = 175.684	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	RIGAKU RAXIS		2006-04-18	M	SINGLE WAVELENGTH

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

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	2.35	30	100	0.068	12.1	8.1		21011

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	2.35	2.43		100	0.95		7.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB entry 1V8K	2.35	29.285	20965	1077	99.795	0.224	0.2215	0.2833	random	57.036

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]
0.297	0.149		0.297		-0.446

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.455
r_dihedral_angle_4_deg	18.281
r_dihedral_angle_3_deg	14.673
r_dihedral_angle_1_deg	6.419
r_scangle_it	3.862
r_mcangle_it	3.518
r_scbond_it	2.814
r_mcbond_it	2.467
r_angle_refined_deg	1.394
r_nbtor_refined	0.302

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.455
r_dihedral_angle_4_deg	18.281
r_dihedral_angle_3_deg	14.673
r_dihedral_angle_1_deg	6.419
r_scangle_it	3.862
r_mcangle_it	3.518
r_scbond_it	2.814
r_mcbond_it	2.467
r_angle_refined_deg	1.394
r_nbtor_refined	0.302
r_nbd_refined	0.201
r_xyhbond_nbd_refined	0.139
r_symmetry_vdw_refined	0.138
r_symmetry_hbond_refined	0.115
r_chiral_restr	0.09
r_bond_refined_d	0.016
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2516
Nucleic Acid Atoms
Solvent Atoms	25
Heterogen Atoms	31

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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 R01GM133198.