X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GVOPDB ENTRY 3GVO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52910.2M ammonium citrate, 0.2M Li2SO4, 22%(w/v) PEG 4000 , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
3.1260.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 150.54α = 90
b = 150.54β = 90
c = 77.22γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152008-03-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.92DiamondI03

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
12.837.8899.90.08911.55.424770247465.775.5
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)
12.82.951000.4715.75.53595

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3GVO2.837.872349223335125099.330.194570.194570.191510.25317RANDOM63.549
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]
0.190.090.19-0.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.121
r_dihedral_angle_4_deg20.462
r_dihedral_angle_3_deg17.3
r_dihedral_angle_1_deg4.904
r_scangle_it2.168
r_angle_refined_deg1.328
r_scbond_it1.29
r_mcangle_it0.935
r_mcbond_it0.53
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.121
r_dihedral_angle_4_deg20.462
r_dihedral_angle_3_deg17.3
r_dihedral_angle_1_deg4.904
r_scangle_it2.168
r_angle_refined_deg1.328
r_scbond_it1.29
r_mcangle_it0.935
r_mcbond_it0.53
r_nbtor_refined0.307
r_symmetry_vdw_refined0.232
r_nbd_refined0.23
r_symmetry_hbond_refined0.174
r_xyhbond_nbd_refined0.136
r_chiral_restr0.093
r_bond_refined_d0.013
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5552
Nucleic Acid Atoms
Solvent Atoms86
Heterogen Atoms20

Software

Software
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling