X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2HP6PDB ID 2HP6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP92932M ammonium sulfate, Bicine, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6353.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.45α = 90
b = 95.46β = 90
c = 125.67γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayIMAGE PLATEMAR scanner 345 mm plate2005-02-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.54178

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
12.052096.50.10814.75.8361063610627.59
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)
12.052.1692.60.8462.25.74956

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 ID 2HP62.0514.8835412186599.940.212490.209430.27001RANDOM24.671
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]
-0.761.57-0.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.178
r_dihedral_angle_4_deg17.653
r_dihedral_angle_3_deg14.364
r_dihedral_angle_1_deg5.23
r_mcangle_it2.112
r_scangle_it1.954
r_mcbond_it1.402
r_scbond_it1.392
r_angle_refined_deg1.253
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.178
r_dihedral_angle_4_deg17.653
r_dihedral_angle_3_deg14.364
r_dihedral_angle_1_deg5.23
r_mcangle_it2.112
r_scangle_it1.954
r_mcbond_it1.402
r_scbond_it1.392
r_angle_refined_deg1.253
r_nbtor_refined0.304
r_nbd_refined0.209
r_symmetry_vdw_refined0.171
r_xyhbond_nbd_refined0.168
r_symmetry_hbond_refined0.16
r_chiral_restr0.083
r_bond_refined_d0.01
r_gen_planes_refined0.004
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3860
Nucleic Acid Atoms
Solvent Atoms351
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
AMoREphasing