2V5J

Apo Class II aldolase HpcH


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
150.4 M AMMONIUM DIHYDROGEN PHOSPHATE, 30% (V/V) GLYCEROL, pH 5
Crystal Properties
Matthews coefficientSolvent content
2.345

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.92α = 90
b = 128.92β = 90
c = 175.3γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2005-05-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM14ESRFBM14

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
11.640.81000.0733.610.973671-3
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)
11.61.641000.712.510.5

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1DXE1.640.797068929821000.1740.1730.207RANDOM23.27
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]
0.010.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.219
r_dihedral_angle_4_deg14.419
r_dihedral_angle_3_deg12.743
r_dihedral_angle_1_deg5.217
r_scangle_it3.991
r_scbond_it2.495
r_mcangle_it1.485
r_angle_refined_deg1.471
r_mcbond_it0.935
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.219
r_dihedral_angle_4_deg14.419
r_dihedral_angle_3_deg12.743
r_dihedral_angle_1_deg5.217
r_scangle_it3.991
r_scbond_it2.495
r_mcangle_it1.485
r_angle_refined_deg1.471
r_mcbond_it0.935
r_nbtor_refined0.311
r_nbd_refined0.212
r_symmetry_vdw_refined0.199
r_symmetry_hbond_refined0.138
r_xyhbond_nbd_refined0.133
r_chiral_restr0.095
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4007
Nucleic Acid Atoms
Solvent Atoms511
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing