5NLR

Auxiliary activity 9


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5ACH 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP3.52983.5 M NaCl 0.1 M citric acid, pH3.5
Crystal Properties
Matthews coefficientSolvent content
3.2161.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 124.92α = 90
b = 124.92β = 90
c = 124.92γ = 90
Symmetry
Space GroupP 41 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2015-04-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-21.03841MAX III911-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)CC (Half)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
125099.90.2380.99612.3113.223096-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0599.91.640.4981.8511.39

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 REPLACEMENTTHROUGHOUT5ACH25021918119199.880.175070.173030.21095RANDOM24.172
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.623
r_dihedral_angle_4_deg12.762
r_dihedral_angle_3_deg11.817
r_dihedral_angle_1_deg7.169
r_long_range_B_other5.498
r_long_range_B_refined5.491
r_scangle_other3.194
r_mcangle_it2.863
r_mcangle_other2.862
r_scbond_it2.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.623
r_dihedral_angle_4_deg12.762
r_dihedral_angle_3_deg11.817
r_dihedral_angle_1_deg7.169
r_long_range_B_other5.498
r_long_range_B_refined5.491
r_scangle_other3.194
r_mcangle_it2.863
r_mcangle_other2.862
r_scbond_it2.17
r_scbond_other2.169
r_mcbond_it2
r_mcbond_other1.998
r_angle_refined_deg1.91
r_angle_other_deg0.933
r_chiral_restr0.12
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1788
Nucleic Acid Atoms
Solvent Atoms265
Heterogen Atoms75

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing