X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5293100 mM sodium citrate, 15% w/v PEG 6000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3748.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.02α = 90
b = 121.829β = 90
c = 55.041γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210rmirrors2009-06-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.97918APS19-BM

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
11.7550990.0690.069275.44577345773-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.7896.90.6330.6332.24.7

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 REPLACEMENTTHROUGHOUT3RVT1.75504342843428231898.940.170650.168780.20587RANDOM24.238
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]
0.28-1.040.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.664
r_dihedral_angle_4_deg20.102
r_dihedral_angle_3_deg12.442
r_dihedral_angle_1_deg7.066
r_long_range_B_refined6.603
r_long_range_B_other6.353
r_angle_other_deg3.791
r_scangle_other3.666
r_scbond_it2.509
r_scbond_other2.412
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.664
r_dihedral_angle_4_deg20.102
r_dihedral_angle_3_deg12.442
r_dihedral_angle_1_deg7.066
r_long_range_B_refined6.603
r_long_range_B_other6.353
r_angle_other_deg3.791
r_scangle_other3.666
r_scbond_it2.509
r_scbond_other2.412
r_mcangle_it1.903
r_angle_refined_deg1.882
r_mcangle_other1.834
r_mcbond_it1.288
r_mcbond_other1.288
r_chiral_restr0.124
r_gen_planes_other0.02
r_bond_refined_d0.019
r_gen_planes_refined0.011
r_bond_other_d
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3291
Nucleic Acid Atoms
Solvent Atoms445
Heterogen Atoms

Software

Software
Software NamePurpose
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
REFMACrefinement
Cootmodel building
HKL-3000data reduction
HKL-3000data scaling