1P3D | pdb_00001p3d

Crystal Structure of UDP-N-acetylmuramic acid:L-alanine ligase (MurC) in Complex with UMA and ANP.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1P31	PDB ENTRY 1P31

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	295	PEG 4000, isopropanol, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.92	α = 90
b = 87.328	β = 104.86
c = 86.113	γ = 90

Symmetry
Space Group	P 1 21 1

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		2002-09-30	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	1.7	25	96.6	0.046	13.4	4.31	117454	113461	2	2	20.4

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)
	1.7	1.76	90.5		0.542	2.47	4.5	10574

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1P31	1.7	25	107740	107740	5691	96.53	0.16953	0.16953	0.16822	0.17	0.19436	RANDOM	14.505

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]
-1.46		-0.44	1.4		-0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.46
r_scangle_it	2.107
r_scbond_it	1.377
r_angle_refined_deg	1.129
r_mcangle_it	0.642
r_mcbond_it	0.333
r_nbd_refined	0.189
r_symmetry_hbond_refined	0.13
r_symmetry_vdw_refined	0.125
r_xyhbond_nbd_refined	0.094

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.46
r_scangle_it	2.107
r_scbond_it	1.377
r_angle_refined_deg	1.129
r_mcangle_it	0.642
r_mcbond_it	0.333
r_nbd_refined	0.189
r_symmetry_hbond_refined	0.13
r_symmetry_vdw_refined	0.125
r_xyhbond_nbd_refined	0.094
r_chiral_restr	0.084
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7099
Nucleic Acid Atoms
Solvent Atoms	791
Heterogen Atoms	164

Software

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