3QVZ | pdb_00003qvz

Crystal structure of the Zn-RIDC1 complex stabilized by BMOE crosslinks cocrystallized in the presence of Cu(II)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298	100 mM HEPES, 12% PEG 3350, 2.46 mM copper sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.525	α = 90
b = 52.525	β = 90
c = 255.717	γ = 120

Symmetry
Space Group	P 61

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 325 mm CCD		2010-07-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	1.265	SSRL	BL9-2

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	2.5	45.488	97.9	0.12	13.8	15.8	13499	13499

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.64	97		0.545	0.545	1.3	16.7	1947

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	2.64	42.86	11686	11199	795	95.83	0.264	0.2607	0.2755	0.3056	0.3002	RANDOM	22.1402

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]
2.32			2.32		-4.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.959
r_dihedral_angle_3_deg	19.782
r_dihedral_angle_4_deg	19.558
r_dihedral_angle_1_deg	4.965
r_scangle_it	2.584
r_angle_refined_deg	1.73
r_scbond_it	1.607
r_mcangle_it	0.758
r_mcbond_it	0.359
r_chiral_restr	0.108

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.959
r_dihedral_angle_3_deg	19.782
r_dihedral_angle_4_deg	19.558
r_dihedral_angle_1_deg	4.965
r_scangle_it	2.584
r_angle_refined_deg	1.73
r_scbond_it	1.607
r_mcangle_it	0.758
r_mcbond_it	0.359
r_chiral_restr	0.108
r_bond_refined_d	0.022
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3284
Nucleic Acid Atoms
Solvent Atoms	12
Heterogen Atoms	217

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection

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.