2G3I

Structure of S.olivaceoviridis xylanase Q88A/R275A mutant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOthersame protein in different crystal form

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52942.1M ammonium dehydrogen phosphate, 0.1M Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
3.463.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.317α = 90
b = 119.317β = 90
c = 54.355γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2003-04-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.999ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.13099.50.17913.38.425881
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.299.10.5114.25

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTsame protein in different crystal form2.119.8825843261199.540.1560.1550.192RANDOM12.607
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]
0.670.330.67-1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.135
r_dihedral_angle_4_deg23.08
r_dihedral_angle_3_deg13.328
r_dihedral_angle_1_deg6.705
r_scangle_it2.643
r_scbond_it1.79
r_angle_refined_deg1.338
r_mcangle_it1.09
r_mcbond_it0.911
r_angle_other_deg0.875
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.135
r_dihedral_angle_4_deg23.08
r_dihedral_angle_3_deg13.328
r_dihedral_angle_1_deg6.705
r_scangle_it2.643
r_scbond_it1.79
r_angle_refined_deg1.338
r_mcangle_it1.09
r_mcbond_it0.911
r_angle_other_deg0.875
r_symmetry_vdw_other0.257
r_nbd_refined0.213
r_mcbond_other0.185
r_nbd_other0.183
r_xyhbond_nbd_refined0.145
r_symmetry_hbond_refined0.139
r_symmetry_vdw_refined0.115
r_chiral_restr0.085
r_nbtor_other0.084
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2309
Nucleic Acid Atoms
Solvent Atoms233
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling