3CE9 | pdb_00003ce9

Crystal structure of glycerol dehydrogenase (NP_348253.1) from Clostridium acetobutylicum at 2.37 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	NANODROP, 0.2M NaCl, 20.0% PEG 3000, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.74	α = 90
b = 125.81	β = 102.33
c = 133.23	γ = 90

Symmetry
Space Group	C 1 2 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	Adjustable focusing mirrors in K-B geometry	2007-10-26	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.91840, 0.97953, 0.97939	APS	23-ID-D

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	2.37	28.94	96.9	0.05	8.2			66387		-3	53.802

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	2.37	2.45	91.4		0.401	1.8

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	2.37	28.94	66387	3364	98.54	0.189	0.188	0.19	0.214	0.21	RANDOM	40.094

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]
-0.46		-0.55	-0.79		1.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.026
r_dihedral_angle_4_deg	17.442
r_dihedral_angle_3_deg	15.189
r_scangle_it	5.817
r_dihedral_angle_1_deg	4.249
r_scbond_it	3.719
r_mcangle_it	1.979
r_angle_refined_deg	1.33
r_angle_other_deg	1.256
r_mcbond_it	0.987

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.026
r_dihedral_angle_4_deg	17.442
r_dihedral_angle_3_deg	15.189
r_scangle_it	5.817
r_dihedral_angle_1_deg	4.249
r_scbond_it	3.719
r_mcangle_it	1.979
r_angle_refined_deg	1.33
r_angle_other_deg	1.256
r_mcbond_it	0.987
r_mcbond_other	0.236
r_chiral_restr	0.069
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10663
Nucleic Acid Atoms
Solvent Atoms	199
Heterogen Atoms	78

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	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.