X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1N9EPPLO 1N9E chain A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP830035% MPD, Imidazole pH 8.0, 200mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 300K. CRYSTAL EXPOSED TO XENON AT 300 PSI FOR 90 SECONDS THEN FROZEN
Crystal Properties
Matthews coefficientSolvent content
2.5451.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 140.144α = 90
b = 66.702β = 119.24
c = 108.62γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315double crystal monochromator2003-04-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-21.552SSRLBL9-2

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
11.6831.4687.70.0911.99971927
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.681.7484.62.1

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 REPLACEMENTTHROUGHOUTPPLO 1N9E chain A1.6831.4785763170587.710.1510.1510.182RANDOM33.28
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]
-0.010.050.010.05
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free21.586
r_scangle_it10.416
r_scbond_it8.042
r_dihedral_angle_1_deg6.782
r_mcangle_it6.501
r_mcbond_it4.889
r_angle_refined_deg1.403
r_angle_other_deg0.834
r_symmetry_vdw_other0.308
r_nbd_other0.25
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free21.586
r_scangle_it10.416
r_scbond_it8.042
r_dihedral_angle_1_deg6.782
r_mcangle_it6.501
r_mcbond_it4.889
r_angle_refined_deg1.403
r_angle_other_deg0.834
r_symmetry_vdw_other0.308
r_nbd_other0.25
r_nbd_refined0.192
r_symmetry_vdw_refined0.167
r_symmetry_hbond_refined0.135
r_xyhbond_nbd_refined0.12
r_chiral_restr0.093
r_metal_ion_refined0.089
r_nbtor_other0.083
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
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_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5933
Nucleic Acid Atoms
Solvent Atoms632
Heterogen Atoms120

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing