X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NH0PDB entry 1nh0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.22772.0M Ammonium dihydrogen Phospate, 0.1M Tric.Cl pH 8.5, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.4549.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.321α = 90
b = 67.181β = 94.99
c = 42.498γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHFlat pre-mirror, a fixed-exit sagital focusing double Silicon (111) crystal monochromator and a vertical focusing mirror. Both mirrors are Rhodium-coated.2004-03-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.800EMBL/DESY, HAMBURGX13

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
12.145099.90.0559.37.41243143.2
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)
12.142.1999.20.22832.8

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 1nh02.1528.811243164299.980.178640.175920.23258RANDOM38.384
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]
-0.020.05-0.020.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.898
r_dihedral_angle_4_deg18.26
r_dihedral_angle_3_deg16.485
r_dihedral_angle_1_deg7.555
r_scangle_it4.13
r_scbond_it2.674
r_angle_refined_deg1.929
r_mcangle_it1.513
r_mcbond_it0.925
r_chiral_restr0.884
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.898
r_dihedral_angle_4_deg18.26
r_dihedral_angle_3_deg16.485
r_dihedral_angle_1_deg7.555
r_scangle_it4.13
r_scbond_it2.674
r_angle_refined_deg1.929
r_mcangle_it1.513
r_mcbond_it0.925
r_chiral_restr0.884
r_nbtor_refined0.326
r_symmetry_vdw_refined0.273
r_nbd_refined0.227
r_symmetry_hbond_refined0.215
r_xyhbond_nbd_refined0.185
r_bond_refined_d0.009
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1520
Nucleic Acid Atoms
Solvent Atoms202
Heterogen Atoms46

Software

Software
Software NamePurpose
XDSdata scaling
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
XDSdata reduction