1P31 | pdb_00001p31

Crystal Structure of UDP-N-acetylmuramic acid:L-alanine Ligase (MurC) from Haemophilus influenzae

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	nanovolume	8.1	277	PEG 4000, glycerol, magnesium chloride, Tris, pH 8.1, nanovolume, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.523	α = 90
b = 92.274	β = 90
c = 118.174	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 4		2002-07-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3	1.0	ALS	5.0.3

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	1.85	25	90	0.064	10.8	4.45	86600	77944	2	2	13.3

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	1.85	1.89	93		0.45	3	4.5	5314

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.85	25	73241	73241	3868	89.79	0.17135	0.17135	0.16938	0.1729	0.20836	RANDOM	13.859

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]
2.08			-1.65		-0.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.523
r_scangle_it	2.96
r_scbond_it	1.879
r_angle_refined_deg	1.112
r_mcangle_it	0.885
r_mcbond_it	0.443
r_nbd_refined	0.194
r_symmetry_vdw_refined	0.177
r_symmetry_hbond_refined	0.164
r_xyhbond_nbd_refined	0.119

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.523
r_scangle_it	2.96
r_scbond_it	1.879
r_angle_refined_deg	1.112
r_mcangle_it	0.885
r_mcbond_it	0.443
r_nbd_refined	0.194
r_symmetry_vdw_refined	0.177
r_symmetry_hbond_refined	0.164
r_xyhbond_nbd_refined	0.119
r_chiral_restr	0.075
r_bond_refined_d	0.008
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7115
Nucleic Acid Atoms
Solvent Atoms	700
Heterogen Atoms	92

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SHELXS	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.