1HD8 | pdb_00001hd8

Crystal structure of a deacylation-defective mutant of penicillin-binding protein 5 at 2.3 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7		20% POLYETHYLENE GLYCOL 4000, 50 MM TRIS PH 7.0, 0.2 % SODIUM AZIDE

Crystal Properties
Matthews coefficient	Solvent content
3.06	59.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.83	α = 90
b = 50.83	β = 90
c = 140.29	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	293	IMAGE PLATE	MACSCIENCE	MIRRORS	1998-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	NONIUS FR391

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.3	22.4	94.8	0.069	13.2	2.52		17239			28.41

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.38	85.2		0.294	3.3	1.9

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MIR	THROUGHOUT	2.3	15	17184	1693	95.4	0.207	0.199	0.283	RANDOM	35.44

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]

RMS Deviations
Key	Refinement Restraint Deviation
p_transverse_tor	22.8
p_staggered_tor	19.9
p_planar_tor	9.8
p_scangle_it	2.92
p_mcangle_it	2.541
p_scbond_it	1.864
p_mcbond_it	1.642
p_multtor_nbd	0.257
p_singtor_nbd	0.191
p_xyhbond_nbd	0.187
p_chiral_restr	0.148
p_planar_d	0.074
p_angle_d	0.043
p_plane_restr	0.0244
p_bond_d	0.013
p_angle_deg
p_hb_or_metal_coord
p_xhyhbond_nbd
p_orthonormal_tor
p_special_tor

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2606
Nucleic Acid Atoms
Solvent Atoms	145
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing