Experiment: 2GYD

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	0.05 M cadmium sulfate, 0.1 M HEPES, and 1.0 M sodium acetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.23	61.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 181.89	α = 90
b = 181.89	β = 90
c = 181.89	γ = 90

Symmetry
Space Group	F 4 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	CCD	ADSC QUANTUM 315		2005-11-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X6A	0.9791	NSLS	X6A

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	1.72	37.13	99	0.075	16.9	18.94	27676	27676

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	1.72	1.78	93		0.432	2.8	10.12	2547

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	FOURIER SYNTHESIS	THROUGHOUT	1XZ1	1.72	37.13	27673	27673	1409	99.03	0.208	0.208	0.207	0.217	RANDOM	22.533

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.163
r_dihedral_angle_4_deg	21.931
r_dihedral_angle_3_deg	13.64
r_dihedral_angle_1_deg	4.577
r_scangle_it	4.262
r_scbond_it	2.596
r_mcbond_it	1.397
r_mcangle_it	1.395
r_angle_refined_deg	1.097
r_nbtor_refined	0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.163
r_dihedral_angle_4_deg	21.931
r_dihedral_angle_3_deg	13.64
r_dihedral_angle_1_deg	4.577
r_scangle_it	4.262
r_scbond_it	2.596
r_mcbond_it	1.397
r_mcangle_it	1.395
r_angle_refined_deg	1.097
r_nbtor_refined	0.3
r_symmetry_hbond_refined	0.206
r_nbd_refined	0.204
r_symmetry_vdw_refined	0.196
r_xyhbond_nbd_refined	0.183
r_metal_ion_refined	0.133
r_chiral_restr	0.081
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1354
Nucleic Acid Atoms
Solvent Atoms	183
Heterogen Atoms	17

Software

Software
Software Name	Purpose
d*TREK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XTALVIEW	refinement

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.