1GVY

Substrate distorsion by beta-mannanase from Pseudomonas cellulosa


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1J9YPDB ENTRY 1J9Y

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5100MM TRIS PH7.5, 26% PEG550, 9MM ZNSO4, pH 7.50
Crystal Properties
Matthews coefficientSolvent content
2.6953.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.192α = 90
b = 93.192β = 90
c = 54.343γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORS2001-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX14.2SRSPX14.2

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
11.72099.40.06120.373.4850905
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)
11.71.7696.40.1726.752.57

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 1J9Y1.72048658260999.60.1450.1440.17RANDOM14.67
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]
-0.47-0.470.94
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it3.567
r_scbond_it2.262
r_dihedral_angle_3_deg1.995
r_angle_other_deg1.723
r_mcangle_it1.567
r_mcbond_it0.957
r_nbtor_other0.496
r_symmetry_vdw_refined0.233
r_nbd_refined0.226
r_nbd_other0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it3.567
r_scbond_it2.262
r_dihedral_angle_3_deg1.995
r_angle_other_deg1.723
r_mcangle_it1.567
r_mcbond_it0.957
r_nbtor_other0.496
r_symmetry_vdw_refined0.233
r_nbd_refined0.226
r_nbd_other0.2
r_symmetry_vdw_other0.172
r_xyhbond_nbd_refined0.13
r_chiral_restr0.122
r_metal_ion_refined0.109
r_symmetry_hbond_refined0.108
r_xyhbond_nbd_other0.105
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_gen_planes_other0.005
r_bond_other_d0.002
r_angle_refined_deg
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_metal_ion_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 Atoms3012
Nucleic Acid Atoms
Solvent Atoms451
Heterogen Atoms65

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing