2X2O | pdb_00002x2o

The flavoprotein NrdI from Bacillus cereus with the initially oxidized FMN cofactor in an intermediate radiation reduced state

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RLJ	PDB ENTRY 1RLJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		0.1 M SODIUM CACODYLATE TRIHYDRATE PH 6.5, 0.2 M ZINC ACETATE DIHYDRATE, 14 %(W/V) PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.05	40.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.855	α = 90
b = 45.765	β = 90
c = 56.745	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	IMAGE PLATE	MAR scanner 345 mm plate		2009-02-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM1A		ESRF	BM1A

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	1.13	34.2	100	0.06	13.8	4.5		42556

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	1.13	1.19	100		0.49	2.8	4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	PDB ENTRY 1RLJ	1.13	30	40337		94.9	0.1436		0.14	0.173	0.17	RANDOM

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]

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
9	920	1131.18

RMS Deviations
Key	Refinement Restraint Deviation
s_approx_iso_adps	0.101
s_non_zero_chiral_vol	0.079
s_zero_chiral_vol	0.069
s_angle_d	0.032
s_anti_bump_dis_restr	0.032
s_similar_adp_cmpnt	0.032
s_from_restr_planes	0.0319
s_bond_d	0.013
s_rigid_bond_adp_cmpnt	0.004
s_similar_dist

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	934
Nucleic Acid Atoms
Solvent Atoms	158
Heterogen Atoms	40

Software

Software
Software Name	Purpose
SHELXL-97	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	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.