7PNH | pdb_00007pnh

X-ray structure of the adduct formed upon reaction of Pt(II) complex 2c with lysozyme

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	193L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4	293	20% ethylene glycol 0.1 M sodium acetate buffer pH 4.0 0.6 M sodium nitrate

Crystal Properties
Matthews coefficient	Solvent content
2	38.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.2	α = 90
b = 77.2	β = 90
c = 38.53	γ = 90

Symmetry
Space Group	P 43 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 PILATUS3 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	1.22	34.52	100	0.056	0.057	0.012	1	24.5	23.2		35283

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	1.22	1.24	100		1.531	1.564	0.315	0.861	2.2	24.3

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	193L	1.22	34.52	33997	1687	96.489	0.135	0.1328	0.14	0.1741	0.17	20.279

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]
0.52			0.52		-1.039

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.553
r_dihedral_angle_4_deg	23.768
r_dihedral_angle_3_deg	13.024
r_rigid_bond_restr	8.909
r_dihedral_angle_1_deg	6.312
r_lrange_it	5.46
r_lrange_other	5.458
r_scangle_it	4.847
r_scangle_other	4.844
r_scbond_it	4.492
r_scbond_other	4.488
r_angle_refined_deg	2.273
r_mcangle_other	2.217
r_mcangle_it	2.215
r_angle_other_deg	1.917
r_mcbond_it	1.788
r_mcbond_other	1.734
r_symmetry_nbd_refined	0.268
r_xyhbond_nbd_refined	0.253
r_nbd_other	0.246
r_nbd_refined	0.226
r_symmetry_xyhbond_nbd_refined	0.217
r_symmetry_nbd_other	0.212
r_nbtor_refined	0.178
r_chiral_restr	0.14
r_symmetry_xyhbond_nbd_other	0.093
r_symmetry_nbtor_other	0.083
r_xyhbond_nbd_other	0.058
r_ext_dist_refined_d	0.041
r_bond_refined_d	0.02
r_metal_ion_refined	0.02
r_bond_other_d	0.018
r_gen_planes_refined	0.013
r_gen_planes_other	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	177
Heterogen Atoms	49

Software

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