5IDD | pdb_00005idd

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

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	4.7	293	CRYSTALLIZATION CONDITIONS: 40MG HEWL (2.7MM) CO-CRYSTALLISED WITH 3MG CARBOPLATIN (8.1MM). 462.5 microL OF A 0.02M NAAC SOLUTION ALONG REMARK 280 WITH 462.5 microL OF A 0.5M NANO3 SOLUTION WAS USED WITH 75 microL DMSO.

Crystal Properties
Matthews coefficient	Solvent content
1.79	31.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 26.957	α = 88.76
b = 31.794	β = 71.99
c = 34.055	γ = 68.33

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	CONFOCAL MIRROR OPTICS	2012-11-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR-H	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	1.13	32.21	94.1	0.086	7.2	2.9		35817

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	1.13	1.16	77		0.31	2	1.1

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	4oxe	1.13	32.21	33282	1762	94.09	0.17964	0.1775	0.18	0.21982	0.22	RANDOM	12.268

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.443
r_sphericity_free	27.301
r_dihedral_angle_4_deg	19.942
r_sphericity_bonded	11.116
r_dihedral_angle_3_deg	10.158
r_rigid_bond_restr	8.793
r_dihedral_angle_1_deg	6.948
r_scangle_other	4.131
r_long_range_B_refined	3.87
r_long_range_B_other	3.869
r_scbond_it	3.526
r_scbond_other	3.523
r_mcangle_other	2.77
r_mcangle_it	2.602
r_mcbond_it	2.096
r_angle_refined_deg	2.056
r_mcbond_other	1.869
r_angle_other_deg	1.044
r_chiral_restr	0.149
r_bond_refined_d	0.021
r_gen_planes_refined	0.012
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	986
Nucleic Acid Atoms
Solvent Atoms	79
Heterogen Atoms	41

Software

Software
Software Name	Purpose
REFMAC	refinement
SAINT	data reduction
APEX 2	data scaling
PHASER	phasing