5GHY | pdb_00005ghy

Crystal structure of beta-lactamase PenP mutant-E166H in complex with cephaloridine as "post-acylation" intermediate

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		289	0.1M Tris pH 8.0, 22.5% PEG 3350, 0.4M ammonium acetate

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.24	α = 76.84
b = 45.94	β = 75.58
c = 65.99	γ = 69.07

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	IMAGE PLATE	RIGAKU RAXIS IV++		2013-09-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.005	63.155	93.3	0.068	0.079	0.04	14.2	3.9	28415	28415

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)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.01	2.11	89.1		0.239	0.239	0.276	0.139	3.2	3.9	3964

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	2.1	38	23641	1263	93.95	0.1982	0.1958	0.2	0.2404	0.24	RANDOM	21.174

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]
0.09	-0.03	0.08	-0.03	-0.02	-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.618
r_dihedral_angle_4_deg	15.365
r_dihedral_angle_3_deg	15.113
r_dihedral_angle_1_deg	7.237
r_angle_refined_deg	1.173
r_angle_other_deg	0.676
r_chiral_restr	0.074
r_gen_planes_refined	0.011
r_bond_refined_d	0.007
r_bond_other_d	0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.618
r_dihedral_angle_4_deg	15.365
r_dihedral_angle_3_deg	15.113
r_dihedral_angle_1_deg	7.237
r_angle_refined_deg	1.173
r_angle_other_deg	0.676
r_chiral_restr	0.074
r_gen_planes_refined	0.011
r_bond_refined_d	0.007
r_bond_other_d	0.006
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4008
Nucleic Acid Atoms
Solvent Atoms	145
Heterogen Atoms	44

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data collection
PDB_EXTRACT	data extraction
SCALA	data reduction
SCALA	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.