5HQ1 | pdb_00005hq1

Comment on S. W. M. Tanley and J. R. Helliwell Structural dynamics of cisplatin binding to histidine in a protein Struct. Dyn. 1, 034701 (2014) regarding the refinement of 4mwk, 4mwm, 4mwn and 4oxe and the method we have adopted.

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	4.7	294	CRYSTALLIZATION CONDITIONS: 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, BATCH, TEMPERATURE 294K, PH 4.7, EVAPORATION.

Crystal Properties
Matthews coefficient	Solvent content
1.74	29.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 26.777	α = 88.9
b = 31.382	β = 72.31
c = 33.865	γ = 68.46

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	200	CCD	APEX II CCD		2012-11-03	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)	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	32.09	90.8	0.0875	5.93	2.25		47695			7.4

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	1.1	79.7		0.2408	1.33	0.81

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	MOLECULAR REPLACEMENT	THROUGHOUT	4mwm	1	32.09	45284	2410	90.8	0.17317	0.17188	0.1773	0.19699	0.2047	RANDOM	11.704

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]
0.38	0.14	-0.87	-0.27	0.54	-0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.027
r_sphericity_free	27.127
r_dihedral_angle_4_deg	16.472
r_sphericity_bonded	12.287
r_dihedral_angle_3_deg	10.297
r_dihedral_angle_1_deg	6.963
r_rigid_bond_restr	6.1
r_scangle_other	4.517
r_scbond_other	3.804
r_scbond_it	3.773
r_long_range_B_refined	3.606
r_long_range_B_other	3.532
r_mcangle_it	2.31
r_mcangle_other	2.308
r_mcbond_other	1.922
r_mcbond_it	1.921
r_angle_refined_deg	1.908
r_angle_other_deg	0.977
r_chiral_restr	0.139
r_bond_refined_d	0.023
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	976
Nucleic Acid Atoms
Solvent Atoms	91
Heterogen Atoms	27

Software

Software
Software Name	Purpose
REFMAC	refinement
SAINT	data reduction
APEX	data scaling
PHASER	phasing