3NOL

Crystal structure of Zymomonas mobilis Glutaminyl Cyclase (trigonal form)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2IWAPDB ENTRY 2IWA

Crystallization

Crystal Properties
Matthews coefficientSolvent content
1.8132.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.423α = 90
b = 61.423β = 90
c = 98.8γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayIMAGE PLATERIGAKU RAXIS IV++confocal2007-09-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

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
11.753.22599.90.0860.086218.42436524365
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.791000.5360.5360.5740.2011.483510

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 2IWA1.722.4624339124199.910.17980.17770.2202RANDOM11.9369
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]
0.230.110.23-0.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.269
r_dihedral_angle_4_deg15.66
r_dihedral_angle_3_deg11.921
r_dihedral_angle_1_deg6.936
r_scangle_it2.878
r_scbond_it1.895
r_angle_refined_deg1.395
r_mcangle_it1.17
r_mcbond_it0.743
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.269
r_dihedral_angle_4_deg15.66
r_dihedral_angle_3_deg11.921
r_dihedral_angle_1_deg6.936
r_scangle_it2.878
r_scbond_it1.895
r_angle_refined_deg1.395
r_mcangle_it1.17
r_mcbond_it0.743
r_nbtor_refined0.307
r_symmetry_vdw_refined0.221
r_nbd_refined0.193
r_xyhbond_nbd_refined0.118
r_symmetry_hbond_refined0.109
r_chiral_restr0.09
r_metal_ion_refined0.079
r_bond_refined_d0.013
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1897
Nucleic Acid Atoms
Solvent Atoms261
Heterogen Atoms18

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection