2ZYC | pdb_00002zyc

Crystal structure of peptidoglycan hydrolase from Sphingomonas sp. A1

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	1.0M Ammonium phosphate, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.28	α = 90
b = 54.28	β = 90
c = 102.75	γ = 90

Symmetry
Space Group	P 43 21 2

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	RIGAKU JUPITER 210	mirror	2008-05-20	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	RIGAKU JUPITER 210	mirror	2008-05-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.0000	SPring-8	BL38B1
2	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.0395	SPring-8	BL38B1

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
1,2	1.74	30	100	0.055	14.6	10.8		16510

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)
	1.74	1.8	99.9		0.396	4.28	9.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	1.74	28.97	15603	832	99.99	0.201	0.19901	0.1986	0.23777	0.2365	RANDOM	20.107

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]
-0.67			-0.67		1.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.651
r_dihedral_angle_4_deg	20.573
r_dihedral_angle_3_deg	12.909
r_dihedral_angle_1_deg	3.931
r_scangle_it	2.306
r_scbond_it	1.404
r_mcangle_it	1.065
r_angle_refined_deg	1.019
r_mcbond_it	0.646
r_nbtor_refined	0.301
r_nbd_refined	0.195
r_symmetry_vdw_refined	0.17
r_xyhbond_nbd_refined	0.133
r_symmetry_hbond_refined	0.118
r_chiral_restr	0.068
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1309
Nucleic Acid Atoms
Solvent Atoms	184
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXDE	phasing