1NJ4

Crystal structure of a deacylation-defective mutant of penicillin-binding protein 5 at 1.9 A resolution

X-RAY DIFFRACTION

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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	7	293	20% PEG 4000, 100 mM Tris pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.2	α = 90
b = 50.2	β = 90
c = 135.76	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	2002-10-08	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	1.9	36.6	98.7	0.073	7.1	6		29772			25.9

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)
	1.9	1.97	88.4		0.354	1.8	3.4	3024

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	Refinement from a lower resolution structure	THROUGHOUT	PDB ENTRY 1HD8	1.9	15	29705	29705	1507	98.7	0.2091	0.20913	0.20727	0.24454	RANDOM	29.263

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]
-0.34	-0.17		-0.34		0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.483
r_dihedral_angle_1_deg	3.332
r_scangle_it	2.757
r_scbond_it	1.633
r_angle_refined_deg	1.212
r_mcangle_it	1.187
r_mcbond_it	0.62
r_nbd_refined	0.224
r_symmetry_vdw_refined	0.177
r_xyhbond_nbd_refined	0.169
r_symmetry_hbond_refined	0.107
r_chiral_restr	0.085
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2649
Nucleic Acid Atoms
Solvent Atoms	219
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
d*TREK	data scaling