7PNI | pdb_00007pni

X-ray structure of the adduct formed upon reaction of Pt(II) complex 2c 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	22% PEG4K 10 mM sodium citrate pH 5.1

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.14	α = 90
b = 31.79	β = 90.347
c = 73.74	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		2021-03-04	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)	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	2.13	28.04	99	0.078	0.086	0.034	0.998	14.5	6.2		13153

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	2.13	2.17	97.3		0.643	0.721	0.318	0.898	2.3	4.9

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	1jvt	2.13	28.04	13128	674	98.183	0.197	0.1923	0.2	0.275	0.28	39.806

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]
-0.143		-0.192	-0.072		0.217

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.316
r_dihedral_angle_3_deg	15.553
r_dihedral_angle_4_deg	15.093
r_lrange_it	9.283
r_lrange_other	9.28
r_dihedral_angle_1_deg	7.775
r_scangle_it	6.656
r_scangle_other	6.465
r_mcangle_it	6.109
r_mcangle_other	6.105
r_scbond_it	4.178
r_scbond_other	4.174
r_mcbond_other	3.913
r_mcbond_it	3.912
r_angle_refined_deg	2.195
r_angle_other_deg	1.322
r_nbd_other	0.223
r_nbd_refined	0.206
r_xyhbond_nbd_refined	0.204
r_symmetry_nbd_refined	0.198
r_symmetry_nbd_other	0.187
r_symmetry_xyhbond_nbd_refined	0.168
r_nbtor_refined	0.16
r_symmetry_xyhbond_nbd_other	0.136
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.073
r_xyhbond_nbd_other	0.028
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
r_ext_dist_refined_d	0.004
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1885
Nucleic Acid Atoms
Solvent Atoms	139
Heterogen Atoms	5

Software

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