4Q68 | pdb_00004q68

Crystal structure of a N-acetylmuramoyl-L-alanine amidase (BACUNI_02947) from Bacteroides uniformis ATCC 8492 at 1.07 A resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4H4J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	30.00% polyethylene glycol 1500, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.473	α = 90
b = 63.552	β = 90
c = 73.997	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	MARMOSAIC 325 mm CCD	Vertical focusing mirror; double crystal Si(111) monochromator	2014-03-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL14-1		SSRL	BL14-1

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	1.07	46.47	95.9	0.034	22.87	3.93		93219		-3	11.481

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	1.07	1.11	85		0.34	3	2.97

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	MOLECULAR REPLACEMENT	THROUGHOUT	4H4J	1.07	39.355	93156	4687	95.88	0.1117	0.1103	0.12	0.1377	0.15	RANDOM	12.8506

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]
-0.09			-0.18		0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.093
r_sphericity_free	21.348
r_dihedral_angle_4_deg	16.499
r_dihedral_angle_3_deg	11.589
r_sphericity_bonded	6.812
r_dihedral_angle_1_deg	5.728
r_angle_refined_deg	1.362
r_rigid_bond_restr	1.255
r_mcangle_it	1.095
r_mcbond_it	0.812

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.093
r_sphericity_free	21.348
r_dihedral_angle_4_deg	16.499
r_dihedral_angle_3_deg	11.589
r_sphericity_bonded	6.812
r_dihedral_angle_1_deg	5.728
r_angle_refined_deg	1.362
r_rigid_bond_restr	1.255
r_mcangle_it	1.095
r_mcbond_it	0.812
r_mcbond_other	0.788
r_angle_other_deg	0.774
r_chiral_restr	0.088
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1831
Nucleic Acid Atoms
Solvent Atoms	576
Heterogen Atoms	18

Software

Software
Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
XSCALE	data scaling
REFMAC	refinement
XDS	data reduction
MOLREP	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.