1NZU

Wild-type penicillin-binding protein 5 from E. coli modified by beta-mercaptoethanol

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	294	24% PEG 4000, 100 mM magnesium acetate, 100 mM sodium citrate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.22	α = 90
b = 50.22	β = 90
c = 138.25	γ = 120

Symmetry
Space Group	P 32

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV	mirrors	2001-07-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	41.5	99.9	0.065	6.1	2.8	26382	26382			30.37

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2	2.07	99.8		0.308	2	2.7	2657

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	PDB ENTRY 1HD8	2	14.84	26273	26273	2650	99.9	0.2241	0.2241	0.21926	0.26617	RANDOM	32.775

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		0.01		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	19.047
r_dihedral_angle_1_deg	3.506
r_scangle_it	2.723
r_scbond_it	1.659
r_angle_refined_deg	1.332
r_mcangle_it	1.118
r_mcbond_it	0.591
r_nbd_refined	0.237
r_symmetry_vdw_refined	0.218
r_xyhbond_nbd_refined	0.207

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	19.047
r_dihedral_angle_1_deg	3.506
r_scangle_it	2.723
r_scbond_it	1.659
r_angle_refined_deg	1.332
r_mcangle_it	1.118
r_mcbond_it	0.591
r_nbd_refined	0.237
r_symmetry_vdw_refined	0.218
r_xyhbond_nbd_refined	0.207
r_symmetry_hbond_refined	0.139
r_chiral_restr	0.095
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2681
Nucleic Acid Atoms
Solvent Atoms	174
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.