X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NB0PDB ENTRY 1NB0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5293NA CACODALYTE, MG ACETATE, PEG 8000 , pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0539.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.097α = 90
b = 57.097β = 90
c = 82.482γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVOSMIC MIRROR2002-09-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.83099.30.05321.4414856-328.35
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8695.20.8541.23.4

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 1NB01.828.5513300719940.1880.1860.227RANDOM22.07
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]
0.660.330.66-0.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.754
r_scangle_it4.066
r_scbond_it2.552
r_mcangle_it1.823
r_angle_refined_deg1.666
r_mcbond_it1.017
r_nbd_refined0.219
r_symmetry_vdw_refined0.206
r_xyhbond_nbd_refined0.197
r_symmetry_hbond_refined0.155
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.754
r_scangle_it4.066
r_scbond_it2.552
r_mcangle_it1.823
r_angle_refined_deg1.666
r_mcbond_it1.017
r_nbd_refined0.219
r_symmetry_vdw_refined0.206
r_xyhbond_nbd_refined0.197
r_symmetry_hbond_refined0.155
r_chiral_restr0.114
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1177
Nucleic Acid Atoms
Solvent Atoms108
Heterogen Atoms59

Software

Software
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
HKL-2000data reduction