3CH0 | pdb_00003ch0

Crystal structure of glycerophosphoryl diester phosphodiesterase (YP_677622.1) from Cytophaga hutchinsonii ATCC 33406 at 1.50 A resolution

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	293	NANODROP, 14.0% PEG 4000, 24.227% 2-propanol, 5.0% Glycerol, 0.1M Citric acid pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.532	α = 90
b = 61.211	β = 90
c = 113.699	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	Flat mirror (vertical focusing)	2008-02-04	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837, 0.97910	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.5	29.553	100	0.083	0.083	6.4	3.9		56237			15.783

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.54	100		0.707	0.707	1.1	3.9	4115

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	MAD	THROUGHOUT	1.5	29.553	56166	2816	99.98	0.16	0.158	0.17	0.189	0.19	RANDOM	13.008

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]
0.59			0.09		-0.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.228
r_dihedral_angle_4_deg	19.667
r_dihedral_angle_3_deg	12.457
r_dihedral_angle_1_deg	5.943
r_scangle_it	5.273
r_scbond_it	4.227
r_mcangle_it	2.624
r_mcbond_it	2.112
r_angle_refined_deg	1.655
r_angle_other_deg	0.974
r_mcbond_other	0.521
r_symmetry_vdw_refined	0.266
r_symmetry_vdw_other	0.226
r_nbd_refined	0.211
r_nbd_other	0.195
r_nbtor_refined	0.177
r_xyhbond_nbd_refined	0.147
r_symmetry_hbond_refined	0.136
r_chiral_restr	0.095
r_nbtor_other	0.087
r_bond_refined_d	0.017
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2148
Nucleic Acid Atoms
Solvent Atoms	400
Heterogen Atoms	83

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction