4YEN | pdb_00004yen

Room temperature X-ray diffraction studies of cisplatin binding to HEWL in DMSO media after 14 months of crystal storage - new refinement

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4G4A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	4.7	295	HEWL co-crystallized with cisplatin with 5% DMSO media in 1 mL 10% sodium chloride + 1 ml 0.04 M sodium acetate, pH 4.7

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.113	α = 90
b = 79.113	β = 90
c = 37.985	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	295	CCD	APEX II CCD		2012-01-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	50	100	0.086	0.086	0.092	0.032	8.8	7.9	8602	8602		-3	25.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.03	100		0.571	0.63	0.264	0.865	2.7	5.6	411

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	FOURIER SYNTHESIS	THROUGHOUT	4G4A	2	50	8107	450	99.8	0.1481	0.1464	0.16	0.1788	0.18	RANDOM	28.046

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]
0.06			0.06		-0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.32
r_sphericity_bonded	30.527
r_sphericity_free	25.995
r_dihedral_angle_4_deg	23.506
r_dihedral_angle_3_deg	14.34
r_dihedral_angle_1_deg	6.307
r_angle_refined_deg	1.578
r_mcangle_it	1.54
r_angle_other_deg	1.069
r_mcbond_it	0.906

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.32
r_sphericity_bonded	30.527
r_sphericity_free	25.995
r_dihedral_angle_4_deg	23.506
r_dihedral_angle_3_deg	14.34
r_dihedral_angle_1_deg	6.307
r_angle_refined_deg	1.578
r_mcangle_it	1.54
r_angle_other_deg	1.069
r_mcbond_it	0.906
r_mcbond_other	0.905
r_chiral_restr	0.101
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	995
Nucleic Acid Atoms
Solvent Atoms	75
Heterogen Atoms	11

Software

Software
Software Name	Purpose
REFMAC	refinement
APEX	data collection
HKL-3000	data reduction
HKL-3000	data scaling
Coot	model building
PDB_EXTRACT	data extraction
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.