9HMQ | pdb_00009hmq

X-structure of the adduct formed upon reaction of the diiodido analogue of picoplatin with lysozyme (structure C)

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	7.5	293	2.0 M sodium formate and 0.1 Hepes buffer pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
1.93	36.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.01	α = 90
b = 79.01	β = 90
c = 35.43	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 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	2.25	39.51	99.8	0.104	0.108	0.026	0.998	19.4	18.2		5691

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	2.25	2.28	98		0.5	0.516	0.123	0.939	9.6	9.6

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	2.25	39.51	5637	262	99.121	0.227	0.2242	0.2295	0.2771	0.2744	56.585

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]
-0.039			-0.039		0.078

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.815
r_dihedral_angle_4_deg	21.057
r_dihedral_angle_3_deg	17.404
r_lrange_other	10.762
r_lrange_it	10.759
r_scangle_it	8.968
r_scangle_other	8.094
r_dihedral_angle_1_deg	8.019
r_mcangle_it	6.006
r_mcangle_other	5.977
r_scbond_it	4.887
r_scbond_other	4.877
r_mcbond_it	4.226
r_mcbond_other	4.207
r_angle_refined_deg	1.538
r_angle_other_deg	1.316
r_nbd_refined	0.215
r_symmetry_nbd_other	0.212
r_nbd_other	0.211
r_nbtor_refined	0.166
r_xyhbond_nbd_refined	0.159
r_symmetry_xyhbond_nbd_refined	0.122
r_symmetry_nbd_refined	0.112
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.06
r_ext_dist_refined_d	0.032
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	995
Nucleic Acid Atoms
Solvent Atoms	22
Heterogen Atoms	9

Software

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