2X2O

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)
TypeSourceAccession CodeDetails
experimental modelPDB 1RLJPDB ENTRY 1RLJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.50.1 M SODIUM CACODYLATE TRIHYDRATE PH 6.5, 0.2 M ZINC ACETATE DIHYDRATE, 14 %(W/V) PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.0540.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.855α = 90
b = 45.765β = 90
c = 56.745γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110IMAGE PLATEMAR scanner 345 mm plate2009-02-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM1AESRFBM1A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.1334.21000.0613.84.542556
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.131.191000.492.84

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUEPDB ENTRY 1RLJ1.13304033794.90.14360.173RANDOM
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 MethodRefinement High ResolutionRefinement Low Resolution
99201131.18
RMS Deviations
KeyRefinement Restraint Deviation
s_approx_iso_adps0.101
s_non_zero_chiral_vol0.079
s_zero_chiral_vol0.069
s_angle_d0.032
s_anti_bump_dis_restr0.032
s_similar_adp_cmpnt0.032
s_from_restr_planes0.0319
s_bond_d0.013
s_rigid_bond_adp_cmpnt0.004
s_similar_dist
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms934
Nucleic Acid Atoms
Solvent Atoms158
Heterogen Atoms40

Software

Software
Software NamePurpose
SHELXL-97refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing