4Q5K | pdb_00004q5k

Crystal structure of a N-acetylmuramoyl-L-alanine amidase (BACUNI_02947) from Bacteroides uniformis ATCC 8492 at 1.30 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	29% polyethylene glycol 4000, 0.1mM Tris pH8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.471	α = 90
b = 60.93	β = 90
c = 80.122	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	1.3	40.061	99.9	0.039	20.41	3.99		60273		-3	12.667

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	1.3	1.35	99.9		0.558	2.54	3.94

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	1.3	40.061	60203	2940	99.87	0.1173	0.1156	0.13	0.1494	0.16	RANDOM	17.7834

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]
-0.35			0.26		0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.285
r_sphericity_free	26.12
r_dihedral_angle_4_deg	15.576
r_dihedral_angle_3_deg	11.483
r_sphericity_bonded	8.883
r_dihedral_angle_1_deg	5.854
r_mcangle_it	2.28
r_rigid_bond_restr	1.964
r_mcbond_it	1.648
r_mcbond_other	1.576

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.285
r_sphericity_free	26.12
r_dihedral_angle_4_deg	15.576
r_dihedral_angle_3_deg	11.483
r_sphericity_bonded	8.883
r_dihedral_angle_1_deg	5.854
r_mcangle_it	2.28
r_rigid_bond_restr	1.964
r_mcbond_it	1.648
r_mcbond_other	1.576
r_angle_refined_deg	1.372
r_angle_other_deg	0.771
r_chiral_restr	0.08
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1839
Nucleic Acid Atoms
Solvent Atoms	455
Heterogen Atoms	34

Software

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

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.