2IAB

Crystal structure of a protein with FMN-binding split barrel fold (NP_828636.1) from Streptomyces avermitilis at 2.00 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION,SITTING DROP,NANODROP5.627720.0% iso-Propanol, 20.0% PEG-4000, 0.1M Citrate pH 5.6, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3547.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.89α = 90
b = 87.89β = 90
c = 151.58γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat collimating mirror, toroid focusing mirror2006-06-18MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.91162,0.97936,0.97920SSRLBL9-2

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
1234.0011000.07714.9142407231.69
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)
122.051000.68812.31672

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT234.00124057119699.870.180.180.1780.23RANDOM32.924
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]
0.510.260.51-0.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.587
r_dihedral_angle_4_deg17.765
r_dihedral_angle_3_deg13.724
r_dihedral_angle_1_deg6.928
r_scangle_it6.764
r_scbond_it5.075
r_mcangle_it3.19
r_mcbond_it2.204
r_angle_refined_deg1.636
r_angle_other_deg0.891
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.587
r_dihedral_angle_4_deg17.765
r_dihedral_angle_3_deg13.724
r_dihedral_angle_1_deg6.928
r_scangle_it6.764
r_scbond_it5.075
r_mcangle_it3.19
r_mcbond_it2.204
r_angle_refined_deg1.636
r_angle_other_deg0.891
r_mcbond_other0.79
r_symmetry_vdw_other0.32
r_symmetry_vdw_refined0.224
r_nbd_refined0.213
r_nbd_other0.2
r_symmetry_hbond_refined0.194
r_nbtor_refined0.179
r_xyhbond_nbd_refined0.142
r_chiral_restr0.092
r_nbtor_other0.086
r_bond_refined_d0.018
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2302
Nucleic Acid Atoms
Solvent Atoms234
Heterogen Atoms16

Software

Software
Software NamePurpose
MolProbitymodel building
SOLVEphasing
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction