8OO3 | pdb_00008oo3

X-ray structure of the adduct formed upon reaction of cisplatin with human angiogenin after 5 days soaking

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ANG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.1	293	10% PEG6K, 20 mM sodium citrate pH 5.1, 0.2 M sodium/potassium tartrate

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.32	α = 90
b = 37.48	β = 90
c = 38.33	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		2021-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1.00	ELETTRA	11.2C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.76	42.66	95	0.083	1	19.1	10.7		12229

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.76	1.79	83.2		0.636	0.856	2.3	6.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	THROUGHOUT	1.76	42.66	12114	619	94.893	0.245	0.243	0.25	0.2905	0.3	20.824

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]
-0.149			-0.049		0.198

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.606
r_dihedral_angle_4_deg	17.403
r_dihedral_angle_3_deg	16.088
r_dihedral_angle_1_deg	8.04
r_lrange_it	6.535
r_lrange_other	6.52
r_scangle_it	4.093
r_scangle_other	4.092
r_mcangle_other	3.464
r_mcangle_it	3.46
r_scbond_it	2.577
r_scbond_other	2.561
r_mcbond_it	2.177
r_mcbond_other	2.151
r_angle_refined_deg	1.724
r_angle_other_deg	1.353
r_symmetry_xyhbond_nbd_refined	0.259
r_nbd_other	0.232
r_nbd_refined	0.191
r_symmetry_nbd_other	0.187
r_symmetry_nbd_refined	0.164
r_nbtor_refined	0.159
r_xyhbond_nbd_refined	0.133
r_chiral_restr	0.082
r_symmetry_nbtor_other	0.079
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	985
Nucleic Acid Atoms
Solvent Atoms	94
Heterogen Atoms	18

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing