9HN6 | pdb_00009hn6

X-ray structure of the adduct formed upon reaction of the diiodido analogue of picoplatin with ribonuclease A

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	293	20% PEG4000, and 0.1 M sodium citrate pH 5.1

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.04	α = 90
b = 32.64	β = 90.109
c = 73.45	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		2020-12-05	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)	Rrim I (All)	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	1.77	73.45	99.7	0.077	0.085	0.035	0.997	12	5.7		23489

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.77	1.8	100		0.881	0.966	0.393	0.86	2.4	5.9

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	1.77	73.45	23406	1094	99.254	0.211	0.208	0.2154	0.2761	0.2771	34.929

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]
-0.146		-0.075	0.09		0.057

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.065
r_dihedral_angle_3_deg	13.381
r_dihedral_angle_4_deg	12.891
r_lrange_it	8.156
r_lrange_other	8.109
r_dihedral_angle_1_deg	7.047
r_scangle_it	6.182
r_scangle_other	5.928
r_mcangle_it	4.275
r_mcangle_other	4.268
r_scbond_it	3.524
r_scbond_other	3.52
r_mcbond_it	2.78
r_mcbond_other	2.771
r_angle_refined_deg	1.68
r_angle_other_deg	1.42
r_symmetry_xyhbond_nbd_other	0.317
r_nbd_refined	0.25
r_symmetry_xyhbond_nbd_refined	0.243
r_xyhbond_nbd_refined	0.234
r_symmetry_nbd_refined	0.234
r_symmetry_nbd_other	0.204
r_nbd_other	0.191
r_nbtor_refined	0.157
r_ext_dist_refined_d	0.109
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.072
r_metal_ion_refined	0.041
r_gen_planes_refined	0.016
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	1852
Nucleic Acid Atoms
Solvent Atoms	137
Heterogen Atoms	30

Software

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