7NPM | pdb_00007npm

X-ray structure of the adduct formed upon reaction of oxaliplatin with human angiogenin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5EOP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.1	298	10 % PEG6K, 20 mM sodium citrate pH 5.1, 0.2 M sodium/potassium tartrate

Crystal Properties
Matthews coefficient	Solvent content
1.94	36.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.72	α = 90
b = 85.89	β = 90
c = 33.39	γ = 90

Symmetry
Space Group	P 21 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	DECTRIS PILATUS 6M		2020-11-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	0.96	ELETTRA	11.2C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	1.86	42.945	99.9	0.171	0.052	0.995	10.5	11.8		9691

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.86	1.89	100		1.22	0.387	0.803	2.5	10.7

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5EOP	1.86	42.94	9325	463	96.923	0.182	0.1782	0.19	0.2537	0.26	25.6

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]
0.037			-0.334		0.297

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	23.772
r_dihedral_angle_3_deg	17.12
r_dihedral_angle_4_deg	15.451
r_lrange_it	8.444
r_lrange_other	8.443
r_dihedral_angle_1_deg	6.54
r_scangle_it	5.264
r_scangle_other	5.261
r_mcangle_it	3.932
r_mcangle_other	3.929
r_scbond_it	3.283
r_scbond_other	3.255
r_mcbond_it	2.415
r_mcbond_other	2.413
r_angle_refined_deg	1.628
r_angle_other_deg	1.372
r_symmetry_nbd_refined	0.231
r_symmetry_xyhbond_nbd_refined	0.226
r_nbd_other	0.206
r_xyhbond_nbd_refined	0.197
r_nbd_refined	0.194
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.164
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.072
r_symmetry_xyhbond_nbd_other	0.07
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	976
Nucleic Acid Atoms
Solvent Atoms	83
Heterogen Atoms	13

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing