9EO8 | pdb_00009eo8

X-ray structure of the adduct formed upon reaction of picoplatin with bovine pancreatic ribonuclease (structure D)

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.1	298	22% PEG4000, 0.1 M sodium citrate pH 5.1

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.92	α = 90
b = 32.88	β = 90.308
c = 74	γ = 90

Symmetry
Space Group	C 1 2 1

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		2021-12-04	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	28.83	98.3	0.097	0.996	10	6.2		24352

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	1.81	98.3		0.792	0.792	1.7	6.2

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	FREE R-VALUE	1.76	28.83	24352	1173	99.311	0.199	0.1976	0.21	0.2346	0.24	28.539

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]
-0.07		0.143	-0.048		0.117

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.38
r_dihedral_angle_3_deg	14.286
r_dihedral_angle_4_deg	11.004
r_lrange_it	7.08
r_dihedral_angle_1_deg	7.07
r_lrange_other	7.023
r_scangle_it	5.487
r_scangle_other	5.481
r_mcangle_it	3.639
r_mcangle_other	3.629
r_scbond_it	3.557
r_scbond_other	3.556
r_mcbond_it	2.428
r_mcbond_other	2.428
r_angle_refined_deg	1.605
r_angle_other_deg	1.405
r_metal_ion_refined	0.593
r_symmetry_xyhbond_nbd_refined	0.463
r_symmetry_nbd_refined	0.33
r_nbd_other	0.268
r_nbd_refined	0.223
r_xyhbond_nbd_refined	0.217
r_symmetry_nbd_other	0.193
r_nbtor_refined	0.157
r_ext_dist_refined_d	0.092
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.077
r_gen_planes_refined	0.014
r_bond_refined_d	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1824
Nucleic Acid Atoms
Solvent Atoms	193
Heterogen Atoms	40

Software

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