7RL8 | pdb_00007rl8

Crystal Structure of C79A Mutant of Class D beta-lactamase from Clostridium difficile 630

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6UE2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	292	Protein: 7.2 mg/ml, 0.01M Tris pH 8.3, 5mM DDT; Screen: PACT (D4), 0.1M MMT buffer pH 7.0, 25% (w/v) PEG 1500

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.118	α = 90
b = 93.878	β = 90
c = 138.346	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD	Be	2020-02-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.95	30	100	0.074	0.074	0.08	0.03	25.1	7.4		82125		-3	31.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	1.98	100		0.722	0.722	0.776	0.283	0.844	2.9	7.4

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6ue2	1.95	29.84	78063	3989	99.83	0.1793	0.1778	0.18	0.2066	0.21	RANDOM	39.825

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]
0.96			-0.1		-0.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.795
r_dihedral_angle_3_deg	9.136
r_dihedral_angle_4_deg	9.016
r_dihedral_angle_1_deg	3.134
r_angle_refined_deg	1.242
r_angle_other_deg	0.339
r_chiral_restr	0.061
r_gen_planes_refined	0.054
r_gen_planes_other	0.051
r_bond_refined_d	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.795
r_dihedral_angle_3_deg	9.136
r_dihedral_angle_4_deg	9.016
r_dihedral_angle_1_deg	3.134
r_angle_refined_deg	1.242
r_angle_other_deg	0.339
r_chiral_restr	0.061
r_gen_planes_refined	0.054
r_gen_planes_other	0.051
r_bond_refined_d	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8130
Nucleic Acid Atoms
Solvent Atoms	730
Heterogen Atoms	17

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.