3BIO

Crystal structure of oxidoreductase (Gfo/Idh/MocA family member) from Porphyromonas gingivalis W83

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	294	0.2 M Ammonium acetate, 45% MPD, 0.1M Hepes pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.268	α = 90
b = 99.268	β = 90
c = 356.025	γ = 120

Symmetry
Space Group	H 3 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	ADSC QUANTUM 315	Mirrors	2007-11-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97940	APS	19-ID

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	1.75	30	100	0.105	24	6	68398	68398			15.9

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	1.75	1.78	100		0.81	2.2	5.9

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.8	30	65976	62633	3143	99.26	0.16	0.158	0.156	0.187	RANDOM	16.566

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]
-1.34	-0.67		-1.34		2.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.284
r_dihedral_angle_4_deg	20.536
r_dihedral_angle_3_deg	13.076
r_dihedral_angle_1_deg	6.065
r_scangle_it	3.457
r_scbond_it	2.437
r_angle_refined_deg	1.459
r_mcangle_it	1.217
r_mcbond_it	1.039
r_angle_other_deg	0.968
r_symmetry_vdw_other	0.258
r_mcbond_other	0.229
r_nbd_refined	0.213
r_nbd_other	0.207
r_nbtor_refined	0.168
r_symmetry_hbond_refined	0.141
r_xyhbond_nbd_refined	0.127
r_chiral_restr	0.09
r_nbtor_other	0.085
r_symmetry_vdw_refined	0.058
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4387
Nucleic Acid Atoms
Solvent Atoms	433
Heterogen Atoms	40

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELX	phasing
Coot	model building
MLPHARE	phasing
PHENIX	phasing
REFMAC	phasing
ARP/wARP	model building