X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VPM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.5296200mM Sodium Malonate pH5.5, 18% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties
Matthews coefficientSolvent content
2.1542.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.93α = 90
b = 128.5β = 102.78
c = 83.54γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2013-04-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX2Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.535.3399.135295
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.5699.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1VPM2.535.3333745327261725970.2090.2070.245RANDOM36.16
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]
0.29-0.03-0.290.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.011
r_dihedral_angle_3_deg14.862
r_dihedral_angle_4_deg13.896
r_dihedral_angle_1_deg6.038
r_angle_refined_deg1.474
r_angle_other_deg0.765
r_chiral_restr0.075
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.011
r_dihedral_angle_3_deg14.862
r_dihedral_angle_4_deg13.896
r_dihedral_angle_1_deg6.038
r_angle_refined_deg1.474
r_angle_other_deg0.765
r_chiral_restr0.075
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d0.005
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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 Atoms7704
Nucleic Acid Atoms
Solvent Atoms164
Heterogen Atoms

Software

Software
Software NamePurpose
Blu-Icedata collection
CCP4model building
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing