2O9Z

Crystal Structure of RebH, a FAD-dependent halogenase from Lechevalieria aerocolonigenes, the Apo form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2AQJ2AQJ monomer with no ligands

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP277Protein Solution (18 mg/ml protein, 0.050 M sodium chloride, 0.010 M TRIS pH 8.0) mixed in a 1:1 ratio with the Well Solution (0.9 M K2HPO4, 0.5 M NaH2PO4) Cryoprotected with: well solution supplemented with up to 30% glycerol, vapor diffusion, hanging drop, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.766.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.786α = 90
b = 114.787β = 90
c = 230.584γ = 120
Symmetry
Space GroupP 62

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDAdjustable focusing mirrors in K-B geometry2006-03-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D0.97919APS23-ID-D

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
12.529.1291000.13124.48412.859677
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)
12.52.591000.4328.09510.35912

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2AQJ monomer with no ligands2.49429.12959619300899.9210.1640.1610.208RANDOM2.559
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]
0.9950.4980.995-1.493
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.102
r_dihedral_angle_4_deg18.633
r_dihedral_angle_3_deg14.825
r_dihedral_angle_1_deg6.012
r_scangle_it1.853
r_angle_refined_deg1.407
r_scbond_it1.1
r_nbtor_refined0.312
r_mcangle_it0.251
r_symmetry_hbond_refined0.246
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.102
r_dihedral_angle_4_deg18.633
r_dihedral_angle_3_deg14.825
r_dihedral_angle_1_deg6.012
r_scangle_it1.853
r_angle_refined_deg1.407
r_scbond_it1.1
r_nbtor_refined0.312
r_mcangle_it0.251
r_symmetry_hbond_refined0.246
r_nbd_refined0.203
r_mcbond_it0.195
r_symmetry_vdw_refined0.153
r_xyhbond_nbd_refined0.141
r_chiral_restr0.1
r_bond_refined_d0.014
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8437
Nucleic Acid Atoms
Solvent Atoms455
Heterogen Atoms10

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction