2OFP | pdb_00002ofp

Crystal structure of Escherichia coli ketopantoate reductase in a ternary complex with NADP+ and pantoate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1KS9	PDB entries 1KS9 and 1YJQ
experimental model	PDB	1YJQ	PDB entries 1KS9 and 1YJQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.6	293	50mM HEPES-HCl, 35% v/v dioxane, 2 mM NADP+, 10 mM pantoate, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.09	60.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.692	α = 90
b = 101.692	β = 90
c = 171.168	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		2006-05-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.977	ESRF	ID14-4

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	2.3	50	99.9	0.073	0.073	12.8	9.3	40670	40629			38.8

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)
	2.3	2.35	100		0.425	0.425		9.3	40629

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entries 1KS9 and 1YJQ	2.3	43.94	38533	2032	99.92	0.1592	0.15621	0.15	0.215	0.21	RANDOM	36.301

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]
					0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.219
r_dihedral_angle_4_deg	18.431
r_dihedral_angle_3_deg	16.253
r_dihedral_angle_1_deg	5.975
r_scangle_it	5.385
r_mcangle_it	4.149
r_scbond_it	3.972
r_mcbond_it	3.04
r_angle_refined_deg	1.448
r_nbtor_refined	0.301

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.219
r_dihedral_angle_4_deg	18.431
r_dihedral_angle_3_deg	16.253
r_dihedral_angle_1_deg	5.975
r_scangle_it	5.385
r_mcangle_it	4.149
r_scbond_it	3.972
r_mcbond_it	3.04
r_angle_refined_deg	1.448
r_nbtor_refined	0.301
r_symmetry_hbond_refined	0.241
r_nbd_refined	0.202
r_symmetry_vdw_refined	0.194
r_xyhbond_nbd_refined	0.173
r_chiral_restr	0.095
r_bond_refined_d	0.014
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4703
Nucleic Acid Atoms
Solvent Atoms	508
Heterogen Atoms	144

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	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.