X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2NRLPDB entry 2NRL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.62930.2 M potassium/sodium tartrate, 0.1 M sodium citrate, 2.0 M ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1442.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.008α = 90
b = 51.894β = 103.95
c = 38.644γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2006-06-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.92APS31-ID

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
10.9117.2793.740.05631.215.988244827202
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)
10.910.93487.340.3015.95.5

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONRIGID BODY refinementTHROUGHOUTPDB entry 2NRL0.9117.278824482720435693.740.120680.120020.13324RANDOM7.658
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]
4.674.66-1.96-2.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.146
r_dihedral_angle_4_deg17.109
r_dihedral_angle_3_deg13.671
r_scangle_it6.236
r_dihedral_angle_1_deg4.996
r_scbond_it4.823
r_mcangle_it3.324
r_angle_refined_deg2.43
r_mcbond_it2.278
r_rigid_bond_restr2.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.146
r_dihedral_angle_4_deg17.109
r_dihedral_angle_3_deg13.671
r_scangle_it6.236
r_dihedral_angle_1_deg4.996
r_scbond_it4.823
r_mcangle_it3.324
r_angle_refined_deg2.43
r_mcbond_it2.278
r_rigid_bond_restr2.25
r_angle_other_deg1.152
r_mcbond_other0.961
r_chiral_restr0.128
r_bond_refined_d0.03
r_gen_planes_refined0.013
r_bond_other_d0.007
r_gen_planes_other0.003
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1091
Nucleic Acid Atoms
Solvent Atoms168
Heterogen Atoms70

Software

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