X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VGBPDB ENTRY 2VGB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.4pH 6.4
Crystal Properties
Matthews coefficientSolvent content
2.5250.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.036α = 90
b = 171.795β = 91.17
c = 85.086γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2001-07-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7AEMBL/DESY, HAMBURGBW7A

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
12.72092.60.15.52.150701
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)
12.72.890.10.472.11.6

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 2VGB2.74205070075992.60.2540.2530.294RANDOM58.18
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]
0.73-1.04-0.46-0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.325
r_dihedral_angle_4_deg22.87
r_dihedral_angle_3_deg21.428
r_dihedral_angle_1_deg5.463
r_scangle_it3.275
r_scbond_it1.966
r_angle_refined_deg1.952
r_mcangle_it1.153
r_mcbond_it0.593
r_symmetry_vdw_refined0.477
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.325
r_dihedral_angle_4_deg22.87
r_dihedral_angle_3_deg21.428
r_dihedral_angle_1_deg5.463
r_scangle_it3.275
r_scbond_it1.966
r_angle_refined_deg1.952
r_mcangle_it1.153
r_mcbond_it0.593
r_symmetry_vdw_refined0.477
r_symmetry_hbond_refined0.373
r_nbtor_refined0.342
r_nbd_refined0.293
r_xyhbond_nbd_refined0.193
r_chiral_restr0.115
r_bond_refined_d0.025
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
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 Atoms15181
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms124

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
CCP4phasing