3EGO | pdb_00003ego

Crystal structure of Probable 2-dehydropantoate 2-reductase panE from Bacillus Subtilis

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	298	20% PEG 3k, 0.1M Tris HCl pH 7.0, 0.2M Calcium Acetate monohydrate, Vapor diffusion, Sitting drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 160.86	α = 90
b = 43.658	β = 98.26
c = 83.757	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	ADSC QUANTUM 315		2008-07-10		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.979	NSLS	X29A

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	1.9	50	99.9	0.066	0.051	34.48	7.4	45902	45902

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)
	1.9	1.97	99.9		0.572	0.45	3.36	7.5	8903

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 (All)	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		THROUGHOUT	1.9	50	45889	2322	99.6	0.207	0.207	0.204	0.2032	0.26	0.2591	RANDOM	36.462

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]
-1.42		-0.65	2.36		-1.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.331
r_dihedral_angle_4_deg	20.73
r_dihedral_angle_3_deg	15.651
r_scangle_it	6.809
r_dihedral_angle_1_deg	5.328
r_scbond_it	4.659
r_mcangle_it	3.128
r_mcbond_it	2.155
r_angle_refined_deg	1.398
r_nbtor_refined	0.323

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.331
r_dihedral_angle_4_deg	20.73
r_dihedral_angle_3_deg	15.651
r_scangle_it	6.809
r_dihedral_angle_1_deg	5.328
r_scbond_it	4.659
r_mcangle_it	3.128
r_mcbond_it	2.155
r_angle_refined_deg	1.398
r_nbtor_refined	0.323
r_symmetry_vdw_refined	0.277
r_symmetry_hbond_refined	0.252
r_nbd_refined	0.224
r_xyhbond_nbd_refined	0.192
r_chiral_restr	0.102
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4596
Nucleic Acid Atoms
Solvent Atoms	202
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
SHELXCD	phasing
SHELXE	model building
CCP4	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.