3DO1

Thermolysin by Classical hanging drop method before high X-Ray dose on ESRF ID14-2 beamline


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KEIPDB ENTRY 1KEI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6293DMSO, Ammonium sulfate, MES, hanging drop, 293K, pH6.0, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.3146.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.526α = 90
b = 92.526β = 90
c = 128.553γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC QUANTUM 4Toroidal mirror2007-05-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.93ESRFID14-2

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
11.3380.13810.2430.24335.264020
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)
1.311.3824.10.6740.673841.42697

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 1KEI1.3368.0441554203155.530.2330.2310.277RANDOM21.019
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]
-0.5-0.25-0.50.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.669
r_dihedral_angle_4_deg14.543
r_dihedral_angle_3_deg14.236
r_dihedral_angle_1_deg5.38
r_scangle_it2.3
r_scbond_it1.615
r_angle_refined_deg1.167
r_mcangle_it0.916
r_mcbond_it0.559
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.669
r_dihedral_angle_4_deg14.543
r_dihedral_angle_3_deg14.236
r_dihedral_angle_1_deg5.38
r_scangle_it2.3
r_scbond_it1.615
r_angle_refined_deg1.167
r_mcangle_it0.916
r_mcbond_it0.559
r_nbtor_refined0.305
r_symmetry_hbond_refined0.255
r_nbd_refined0.205
r_symmetry_vdw_refined0.199
r_xyhbond_nbd_refined0.163
r_chiral_restr0.083
r_metal_ion_refined0.061
r_bond_refined_d0.011
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2479
Nucleic Acid Atoms
Solvent Atoms185
Heterogen Atoms22

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
REFMACphasing