X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1H1DPDB ENTRY 1H1D

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.58% PEG6K, 0.1 M MES PH 6.0
Crystal Properties
Matthews coefficientSolvent content
2.653

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.767α = 90
b = 79.627β = 91.14
c = 61.54γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
11.624.4299.90.0521.63.567299
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)
11.61.6498.20.43.2

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 1H1D1.662.026364833961000.1510.1490.178RANDOM15.37
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]
0.7-0.54-1.060.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.487
r_scangle_it3.846
r_scbond_it2.376
r_angle_refined_deg1.74
r_mcangle_it1.514
r_angle_other_deg0.908
r_mcbond_it0.867
r_symmetry_vdw_other0.283
r_nbd_other0.247
r_nbd_refined0.222
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.487
r_scangle_it3.846
r_scbond_it2.376
r_angle_refined_deg1.74
r_mcangle_it1.514
r_angle_other_deg0.908
r_mcbond_it0.867
r_symmetry_vdw_other0.283
r_nbd_other0.247
r_nbd_refined0.222
r_symmetry_hbond_refined0.159
r_xyhbond_nbd_refined0.158
r_symmetry_vdw_refined0.155
r_chiral_restr0.117
r_nbtor_other0.079
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_gen_planes_other0.004
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_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 Atoms3369
Nucleic Acid Atoms
Solvent Atoms554
Heterogen Atoms124

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing