4JBF | pdb_00004jbf

Crystal structure of peptidoglycan glycosyltransferase from Atopobium parvulum DSM 20469.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	0.2 M Ammonium Chloride, 0.1 M HEPES pH 7, 20% PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.927	α = 90
b = 70.167	β = 97.35
c = 114.82	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	MARMOSAIC 300 mm CCD	MIRROR	2013-01-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	1.92	30	99.8	0.124	14.2	3.8	77602	77602		-3	35.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	1.98	99.9		2.75	3.7

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.92	29.48	75977	75977	4010	98.52	0.19746	0.1954	0.192	0.23679	0.2261	RANDOM	40.439

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]
57.11		19.01	-44.57		-12.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.309
r_dihedral_angle_4_deg	11.289
r_dihedral_angle_3_deg	10.278
r_dihedral_angle_1_deg	3.166
r_angle_refined_deg	1.835
r_angle_other_deg	0.84
r_chiral_restr	0.113
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5876
Nucleic Acid Atoms
Solvent Atoms	465
Heterogen Atoms	7

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing