2O7P | pdb_00002o7p

The crystal structure of RibD from Escherichia coli in complex with the oxidised NADP+ cofactor in the active site of the reductase domain

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2G6V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	20mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) at pH 7.4, 150mM NaCl, 10mM mercaptoethanol, 10% (v/v) glycerol, 2mM EDTA, 0.1M MES pH 6.5, 3% (v/v) 1,6 Hexandiol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.96	68.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 173	α = 90
b = 173	β = 90
c = 77.8	γ = 120

Symmetry
Space Group	P 31 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		2005-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.2836	ESRF	ID29

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	3	30	99.8	0.084	0.084	15.6	8.5	27098	27042	-3	-3	84

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	3	3.1	100		0.506	0.506	2.5	8.6	2514

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2G6V	3	28.93	27057	25679	1359	99.93	0.21496	0.21496	0.2122	0.23	0.26653	0.28	RANDOM	85.21

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]
-1.03	-0.52		-1.03		1.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.876
r_dihedral_angle_3_deg	23.211
r_dihedral_angle_4_deg	21.071
r_dihedral_angle_1_deg	7.367
r_scangle_it	3.044
r_scbond_it	1.823
r_angle_refined_deg	1.784
r_mcangle_it	1.387
r_mcbond_it	0.866
r_nbtor_refined	0.317

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.876
r_dihedral_angle_3_deg	23.211
r_dihedral_angle_4_deg	21.071
r_dihedral_angle_1_deg	7.367
r_scangle_it	3.044
r_scbond_it	1.823
r_angle_refined_deg	1.784
r_mcangle_it	1.387
r_mcbond_it	0.866
r_nbtor_refined	0.317
r_nbd_refined	0.247
r_symmetry_vdw_refined	0.213
r_xyhbond_nbd_refined	0.183
r_symmetry_hbond_refined	0.147
r_chiral_restr	0.111
r_bond_refined_d	0.017
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5427
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	96

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
XDS	data reduction
XSCALE	data scaling
MOLREP	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.