4YEM

Carboplatin binding to HEWL in NaBr crystallisation conditions studied at an X-ray wavelength of 0.9163A - new refinement

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	4.7	297	co-crystallizing 20 mg ml HEWL with 1.4 mg carboplatin in 75 ml DMSO, 462.5 ml 0.1 M sodium acetate, 462.5 ml 1 M NaBr solution.

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.58	α = 90
b = 78.58	β = 90
c = 37.29	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	100	PIXEL	PSI PILATUS 6M		2013-09-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9163	Diamond	I04

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	1.47	55.56	94.6	0.09	0.09	16.3	10.6	18627	17672	4	2	12.3

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	1.47	1.5	64		0.46	4.2	8.9

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	4XAN	1.47	39.29	17672	933	91.01	0.1077	0.1053	0.1559	RANDOM	14.86

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			-0.1		0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.302
r_sphericity_free	25.729
r_dihedral_angle_4_deg	20.293
r_dihedral_angle_3_deg	13.444
r_sphericity_bonded	10.609
r_dihedral_angle_1_deg	5.846
r_angle_other_deg	1.923
r_rigid_bond_restr	1.871
r_mcangle_it	1.51
r_angle_refined_deg	1.494

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.302
r_sphericity_free	25.729
r_dihedral_angle_4_deg	20.293
r_dihedral_angle_3_deg	13.444
r_sphericity_bonded	10.609
r_dihedral_angle_1_deg	5.846
r_angle_other_deg	1.923
r_rigid_bond_restr	1.871
r_mcangle_it	1.51
r_angle_refined_deg	1.494
r_mcbond_it	1.237
r_mcbond_other	1.188
r_chiral_restr	0.113
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_gen_planes_other	0.006
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	182
Heterogen Atoms	36

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
MOSFLM	data reduction
Aimless	data scaling
Coot	model building
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.