Experiment: 2ZGJ

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2ZGC	PDB ENTRY 2ZGC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	289	0.1M Bicine, 0.2M Li2SO4, 21% PEG3350, pH8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
3.35	63.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.487	α = 90
b = 74.487	β = 90
c = 112.689	γ = 120

Symmetry
Space Group	P 31 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	IMAGE PLATE	RIGAKU RAXIS IV		2007-11-15	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)	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	2.3	50	99.4	0.051	36.1	5.8	16708	16608

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	2.3	2.35	99.4		0.399	3.38	4.9	1080

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2ZGC	2.3	26.45	15700	832	99.52	0.24226	0.23994	0.24	0.28779	0.29	RANDOM	49.105

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]
-0.26	-0.13		-0.26		0.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.499
r_dihedral_angle_4_deg	18.954
r_dihedral_angle_3_deg	18.111
r_dihedral_angle_1_deg	7.625
r_scangle_it	3.714
r_scbond_it	2.543
r_angle_refined_deg	1.859
r_mcangle_it	1.533
r_mcbond_it	0.944
r_nbtor_refined	0.314

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.499
r_dihedral_angle_4_deg	18.954
r_dihedral_angle_3_deg	18.111
r_dihedral_angle_1_deg	7.625
r_scangle_it	3.714
r_scbond_it	2.543
r_angle_refined_deg	1.859
r_mcangle_it	1.533
r_mcbond_it	0.944
r_nbtor_refined	0.314
r_nbd_refined	0.246
r_symmetry_vdw_refined	0.207
r_symmetry_hbond_refined	0.167
r_xyhbond_nbd_refined	0.16
r_chiral_restr	0.124
r_bond_refined_d	0.019
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1796
Nucleic Acid Atoms
Solvent Atoms	98
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	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.