X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529452% Ammonium sulfate, 0.1M Sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.961.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.19α = 90
b = 91.19β = 90
c = 45.77γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93IMAGE PLATERIGAKU RAXIS IVMirror2004-08-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

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
12.3532.398.90.05617.34.484648375
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)
12.352.4399.60.2654.64.3

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 REPLACEMENTTHROUGHOUT1HIK2.5207065665433498.950.213520.213520.210910.26368RANDOM34.463
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]
0.650.65-1.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.613
r_scangle_it3.598
r_scbond_it2.065
r_angle_refined_deg1.4
r_mcangle_it1.367
r_mcbond_it0.705
r_symmetry_vdw_refined0.291
r_symmetry_hbond_refined0.28
r_xyhbond_nbd_refined0.259
r_nbd_refined0.244
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.613
r_scangle_it3.598
r_scbond_it2.065
r_angle_refined_deg1.4
r_mcangle_it1.367
r_mcbond_it0.705
r_symmetry_vdw_refined0.291
r_symmetry_hbond_refined0.28
r_xyhbond_nbd_refined0.259
r_nbd_refined0.244
r_chiral_restr0.088
r_bond_refined_d0.012
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
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 Atoms1042
Nucleic Acid Atoms
Solvent Atoms104
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling
CNSphasing