2QYT

Crystal structure of 2-dehydropantoate 2-reductase from Porphyromonas gingivalis W83

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	289	0.2M Ammonium sulfate, 0.1M MES, 30% PEG MME5000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.577	α = 90
b = 79.577	β = 90
c = 98.26	γ = 90

Symmetry
Space Group	P 41 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	ADSC QUANTUM 315	Mirror	2007-03-02	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97925, 0.97938	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	2.15	62	95.3	0.132	14.5	6.2	16966	16966			24.83

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	2.15	2.2	67.4		0.475	1.8	2.4

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.15	41.81	16055	16055	866	95.33	0.19839	0.19493	0.26479	RANDOM	21.634

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]
-0.94			-0.94		1.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.654
r_dihedral_angle_3_deg	19.52
r_dihedral_angle_4_deg	19.216
r_dihedral_angle_1_deg	6.688
r_scangle_it	3.288
r_scbond_it	2.196
r_angle_refined_deg	1.748
r_mcangle_it	1.486
r_mcbond_it	0.966
r_nbtor_refined	0.309
r_symmetry_vdw_refined	0.257
r_nbd_refined	0.232
r_xyhbond_nbd_refined	0.175
r_symmetry_hbond_refined	0.165
r_chiral_restr	0.117
r_bond_refined_d	0.017
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2241
Nucleic Acid Atoms
Solvent Atoms	147
Heterogen Atoms	45

Software

Software
Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
MLPHARE	phasing
HKL-3000	phasing