4YEA

Crystal structure of cisplatin bound to a human copper chaperone (dimer) - new refinement

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3IWX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	294	1.5 M LITHIUM SULFATE, 0.1M MES, 50 MM NACL, PH 6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K

Crystal Properties
Matthews coefficient	Solvent content
3.24	62.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.289	α = 90
b = 78.289	β = 90
c = 54.335	γ = 120

Symmetry
Space Group	P 65

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	113	CCD	MARRESEARCH		2009-04-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.14	50	99.9	0.078	0.078	23.4	5.6		10562			33.3

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	2.14	2.18	100		0.401	3.5	5.5

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	3iwx	2.14	25.63	10030	503	99.82	0.1621	0.1602	0.1974	RANDOM	36.165

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]
0.1	0.05		0.1		-0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.285
r_sphericity_bonded	17.818
r_dihedral_angle_3_deg	12.75
r_dihedral_angle_4_deg	7.048
r_dihedral_angle_1_deg	6.937
r_angle_refined_deg	1.469
r_mcangle_it	1.015
r_angle_other_deg	0.884
r_mcbond_it	0.627
r_mcbond_other	0.624

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.285
r_sphericity_bonded	17.818
r_dihedral_angle_3_deg	12.75
r_dihedral_angle_4_deg	7.048
r_dihedral_angle_1_deg	6.937
r_angle_refined_deg	1.469
r_mcangle_it	1.015
r_angle_other_deg	0.884
r_mcbond_it	0.627
r_mcbond_other	0.624
r_chiral_restr	0.082
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1012
Nucleic Acid Atoms
Solvent Atoms	112
Heterogen Atoms	16

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
Coot	model building

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.