9EO5 | pdb_00009eo5

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

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	4.5	298	22% PEG4000, 0.1 M sodium citrate pH 5.1

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.75	α = 90
b = 32.69	β = 90.463
c = 73.54	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	1.99	50.424	99.8	0.161	0.988	7.3	5.9		16745

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	1.99	2.08	99.8		0.161	0.638	2.1	5.8

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	1.99	50.424	16617	755	98.641	0.193	0.1909	0.1973	0.2426	0.2492	32.756

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]
0.101		0.134	0.077		-0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.643
r_dihedral_angle_3_deg	16.71
r_dihedral_angle_4_deg	9.212
r_lrange_it	7.712
r_lrange_other	7.639
r_dihedral_angle_1_deg	7.571
r_scangle_it	4.802
r_scangle_other	4.687
r_mcangle_other	4.262
r_mcangle_it	4.259
r_scbond_it	2.98
r_scbond_other	2.978
r_mcbond_other	2.736
r_mcbond_it	2.735
r_angle_refined_deg	1.536
r_angle_other_deg	1.367
r_symmetry_xyhbond_nbd_refined	0.227
r_nbd_refined	0.224
r_nbd_other	0.223
r_xyhbond_nbd_refined	0.216
r_symmetry_nbd_other	0.187
r_symmetry_nbd_refined	0.178
r_nbtor_refined	0.16
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.063
r_ext_dist_refined_d	0.013
r_symmetry_xyhbond_nbd_other	0.013
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1894
Nucleic Acid Atoms
Solvent Atoms	192
Heterogen Atoms	10

Software

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