Experiment: 3GZF

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		292	PEG 5000, ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
3.24	61.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.538	α = 90
b = 127.538	β = 90
c = 42.797	γ = 90

Symmetry
Space Group	P 43

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	MARMOSAIC 225 mm CCD	mirrors	2008-12-12		SAD
2	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD	mirrors	2008-12-20		SINGLE WAVELENGTH
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X12	0.9777	EMBL/DESY, HAMBURG	X12
2	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X12	0.978	EMBL/DESY, HAMBURG	X12

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	2.7	20	99.1	0.053	23.25	6.05		18188		3

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	2.75	2.92	96.6	96.6	0.441	3.68	6.36

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.756	19.95	18174	927	99.84	0.243	0.24	0.3	RANDOM	68.225

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]
-0.01			-0.01		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.169
r_dihedral_angle_4_deg	26.861
r_dihedral_angle_3_deg	17.914
r_dihedral_angle_1_deg	15.983
r_angle_refined_deg	1.613
r_scangle_it	1.379
r_scbond_it	0.899
r_mcangle_it	0.507
r_mcbond_it	0.267
r_chiral_restr	0.091

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.169
r_dihedral_angle_4_deg	26.861
r_dihedral_angle_3_deg	17.914
r_dihedral_angle_1_deg	15.983
r_angle_refined_deg	1.613
r_scangle_it	1.379
r_scbond_it	0.899
r_mcangle_it	0.507
r_mcbond_it	0.267
r_chiral_restr	0.091
r_bond_refined_d	0.012
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3581
Nucleic Acid Atoms
Solvent Atoms	40
Heterogen Atoms	10

Software

Software
Software Name	Purpose
SCALA	data scaling
BP3	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

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.