4YEO | pdb_00004yeo

Triclinic HEWL co-crystallised with cisplatin, studied at a data collection temperature of 150K - new refinement

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	4.7	294	40mg HEWL co-crystallised with 2.6mg cisplatin, with the platinum compounds being in a 3-fold molar excess to the protein. 462.5 ul of a 0.02M NaAc solution along with 462.5 ul of a 0.5M NaNo3 solution was used with 75 ul DMSO added

Crystal Properties
Matthews coefficient	Solvent content
1.89	31.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 26.998	α = 89.08
b = 31.807	β = 72
c = 34.072	γ = 67.81

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	150	CCD	APEX II CCD		2012-12-07	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)	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	0.98	29.28	94.8	0.045	0.045	15.6	3.5		48959		2	6

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	0.98	1.02	51.7		0.209	3.2	0.6

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	4mwk	0.98	29.26	48959	2646	90.56	0.1133	0.1123	0.12	0.1313	0.14	RANDOM	7.982

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]
0.08	0.02	0.12	0.09		-0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.998
r_dihedral_angle_4_deg	13.767
r_sphericity_free	11.165
r_dihedral_angle_3_deg	10.707
r_dihedral_angle_1_deg	6.627
r_sphericity_bonded	6.316
r_rigid_bond_restr	5.396
r_angle_refined_deg	1.711
r_angle_other_deg	1.358
r_mcangle_it	0.948

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.998
r_dihedral_angle_4_deg	13.767
r_sphericity_free	11.165
r_dihedral_angle_3_deg	10.707
r_dihedral_angle_1_deg	6.627
r_sphericity_bonded	6.316
r_rigid_bond_restr	5.396
r_angle_refined_deg	1.711
r_angle_other_deg	1.358
r_mcangle_it	0.948
r_mcbond_it	0.695
r_mcbond_other	0.694
r_chiral_restr	0.103
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_gen_planes_other	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	997
Nucleic Acid Atoms
Solvent Atoms	233
Heterogen Atoms	55

Software

Software
Software Name	Purpose
REFMAC	refinement
SAINT	data reduction
APEX	data scaling
PHASER	phasing
Coot	model building
PDB_EXTRACT	data extraction

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.