3VZ3

Structural insights into substrate and cofactor selection by sp2771


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3JZ4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.8293PEG 5000 MME, tascimate, HEPES, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3247.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.957α = 90
b = 117.181β = 90
c = 181.98γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2012-06-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.075NSLSX29A

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
11.695092.10.04312.28996122
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7375.9

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 REPLACEMENTTHROUGHOUT3JZ41.6942.4189961473591.810.167510.165640.20342RANDOM13.46
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]
0.19-0.18-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.433
r_dihedral_angle_4_deg18.125
r_dihedral_angle_3_deg12.533
r_dihedral_angle_1_deg5.632
r_scangle_it3.244
r_scbond_it2.033
r_angle_refined_deg1.257
r_mcangle_it1.035
r_mcbond_it0.679
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.433
r_dihedral_angle_4_deg18.125
r_dihedral_angle_3_deg12.533
r_dihedral_angle_1_deg5.632
r_scangle_it3.244
r_scbond_it2.033
r_angle_refined_deg1.257
r_mcangle_it1.035
r_mcbond_it0.679
r_nbtor_refined0.307
r_nbd_refined0.199
r_symmetry_vdw_refined0.184
r_symmetry_hbond_refined0.15
r_xyhbond_nbd_refined0.103
r_chiral_restr0.084
r_bond_refined_d0.011
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6890
Nucleic Acid Atoms
Solvent Atoms1149
Heterogen Atoms110

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling