3HWR

Crystal structure of PanE/ApbA family ketopantoate reductase (YP_299159.1) from Ralstonia eutropha JMP134 at 2.15 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.71	277	26.2000% polyethylene glycol 6000, 0.1M Bicine pH 8.71, Additive: 0.001 M dihydro-nicotinamide-adenine-dinucleotide phosphate (NADPH), VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 116.21	α = 90
b = 116.21	β = 90
c = 95.604	γ = 120

Symmetry
Space Group	P 61

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 and horizontal focussing mirrors	2009-01-28	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2009-01-09	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.91837	SSRL	BL12-2
2	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97927,0.91162,0.97912	SSRL	BL9-2

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
1,2	2.15	29.761	99.9	0.111	0.111	4.124	3.7		39885			34.533

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)
1,2	2.15	2.21	100		0.719	0.719	1	3.8	2923

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.15	29.761	39845	2003	99.84	0.186	0.183	0.226	RANDOM	49.293

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]
-1.4	-0.7		-1.4		2.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.557
r_dihedral_angle_4_deg	14.898
r_dihedral_angle_3_deg	12.184
r_scangle_it	6.855
r_scbond_it	5.117
r_dihedral_angle_1_deg	3.328
r_mcangle_it	2.689
r_mcbond_it	1.918
r_angle_refined_deg	1.781
r_angle_other_deg	1.285
r_mcbond_other	0.487
r_symmetry_vdw_other	0.279
r_xyhbond_nbd_other	0.252
r_nbd_refined	0.194
r_symmetry_hbond_refined	0.19
r_xyhbond_nbd_refined	0.189
r_nbd_other	0.177
r_nbtor_refined	0.164
r_symmetry_vdw_refined	0.156
r_chiral_restr	0.09
r_nbtor_other	0.087
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4361
Nucleic Acid Atoms
Solvent Atoms	213
Heterogen Atoms	134

Software

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