5GHZ | pdb_00005ghz

Crystal structure of beta-lactamase PenP mutant-E166H in complex with cephaloridine as "pre-deacylation" 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
1.95	36.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.29	α = 77.81
b = 45.49	β = 75.48
c = 66.1	γ = 68.76

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++		2013-09-14	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	1.926	63.417	91.2	0.055	0.063	0.032	18	3.9	31135	31135

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	1.93	2.03	86.3		0.128	0.128	0.148	0.075	5.8	3.9	4279

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	1.93	37.4	29548	1580	91.22	0.1612	0.1589	0.1682	0.2044	0.2098	RANDOM	15.23

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]
		0.01		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.727
r_dihedral_angle_4_deg	17.16
r_dihedral_angle_3_deg	14.596
r_dihedral_angle_1_deg	7.416
r_angle_refined_deg	1.088
r_angle_other_deg	0.659
r_chiral_restr	0.074
r_gen_planes_refined	0.011
r_bond_refined_d	0.007
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.727
r_dihedral_angle_4_deg	17.16
r_dihedral_angle_3_deg	14.596
r_dihedral_angle_1_deg	7.416
r_angle_refined_deg	1.088
r_angle_other_deg	0.659
r_chiral_restr	0.074
r_gen_planes_refined	0.011
r_bond_refined_d	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	4008
Nucleic Acid Atoms
Solvent Atoms	484
Heterogen Atoms	44

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
SCALA	data reduction
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.