1SDN | pdb_00001sdn

CRYSTAL STRUCTURE OF A DEACYLATION-DEFECTIVE MUTANT OF PENICILLIN-BINDING PROTEIN 5 MODIFIED BY MERCURY

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1HD8	PDB ENTRY 1HD8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	294	24% (w/v) polyethylene glycol 8000, 50mM sodium citrate, 100mM magnesium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.7	α = 90
b = 50.7	β = 90
c = 140.3	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	294	IMAGE PLATE	MAC Science DIP-2000H	mirrors	1998-08-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	ENRAF-NONIUS FR591	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	2.5	25.4	95.6	0.074	11.2	2.53	13482	13482			30.1

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)
	2.5	2.59	88.7		0.203	4.4

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	REFINEMENT	THROUGHOUT	PDB ENTRY 1HD8	2.5	15	13044	13044	688	98.28	0.1744	0.17447	0.17113	0.17	0.24142	0.24	RANDOM	30.141

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]
-0.7	-0.35		-0.7		1.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.006
r_scangle_it	3.267
r_scbond_it	1.865
r_mcangle_it	1.408
r_angle_refined_deg	1.275
r_mcbond_it	0.728
r_nbd_refined	0.196
r_xyhbond_nbd_refined	0.149
r_symmetry_vdw_refined	0.14
r_symmetry_hbond_refined	0.119

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.006
r_scangle_it	3.267
r_scbond_it	1.865
r_mcangle_it	1.408
r_angle_refined_deg	1.275
r_mcbond_it	0.728
r_nbd_refined	0.196
r_xyhbond_nbd_refined	0.149
r_symmetry_vdw_refined	0.14
r_symmetry_hbond_refined	0.119
r_chiral_restr	0.085
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2679
Nucleic Acid Atoms
Solvent Atoms	46
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
NONIUS	data reduction
SCALEPACK	data scaling
CNS	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.