2GD9

Crystal structure of a putative dihydrofolate reductase (bsu40760, yyap) from bacillus subtilis at 2.30 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION,SITTING DROP,NANODROP7.92770.2M (NH4)2HPO4, 20.0% PEG-3350, No Buffer pH 7.9, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.5765.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.915α = 90
b = 64.915β = 90
c = 143.648γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102005-10-12MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.019859, 0.979718ALS8.3.1

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.364.9571000.1140.1146.23.726393
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)RedundancyNumber Unique Reflections (All)
12.32.361000.7470.74713.7

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 DIFFRACTIONMADTHROUGHOUT2.359.1626334136499.930.210.209660.2070.254RANDOM31.972
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]
0.770.77-1.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.179
r_dihedral_angle_3_deg16.373
r_dihedral_angle_4_deg12.522
r_dihedral_angle_1_deg6.871
r_scangle_it2.483
r_scbond_it1.607
r_angle_refined_deg1.524
r_mcangle_it1.17
r_angle_other_deg0.855
r_mcbond_it0.708
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.179
r_dihedral_angle_3_deg16.373
r_dihedral_angle_4_deg12.522
r_dihedral_angle_1_deg6.871
r_scangle_it2.483
r_scbond_it1.607
r_angle_refined_deg1.524
r_mcangle_it1.17
r_angle_other_deg0.855
r_mcbond_it0.708
r_symmetry_vdw_other0.197
r_nbd_other0.181
r_xyhbond_nbd_refined0.179
r_nbtor_refined0.17
r_symmetry_vdw_refined0.168
r_nbd_refined0.164
r_symmetry_hbond_refined0.15
r_mcbond_other0.126
r_nbtor_other0.084
r_chiral_restr0.082
r_bond_refined_d0.016
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2825
Nucleic Acid Atoms
Solvent Atoms155
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling
SHELXDphasing
autoSHARPphasing