X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NY3PDB entry 1NY3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP52961600 mM Sodium Malonate pH 5, 1 % MPD, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties
Matthews coefficientSolvent content
4.5773.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 254.658α = 90
b = 254.658β = 90
c = 254.658γ = 90
Symmetry
Space GroupF 41 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42003-11-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.11.1ALS5.0.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
13.33010421

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 1NY33.3301042151998.380.284190.281710.33701RANDOM127.583
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_deg33.392
r_dihedral_angle_3_deg16.018
r_dihedral_angle_4_deg15.033
r_dihedral_angle_1_deg4.706
r_angle_refined_deg0.882
r_nbtor_refined0.299
r_nbd_refined0.168
r_symmetry_vdw_refined0.143
r_xyhbond_nbd_refined0.117
r_symmetry_hbond_refined0.106
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.392
r_dihedral_angle_3_deg16.018
r_dihedral_angle_4_deg15.033
r_dihedral_angle_1_deg4.706
r_angle_refined_deg0.882
r_nbtor_refined0.299
r_nbd_refined0.168
r_symmetry_vdw_refined0.143
r_xyhbond_nbd_refined0.117
r_symmetry_hbond_refined0.106
r_chiral_restr0.056
r_bond_refined_d0.006
r_gen_planes_refined0.002
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_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2249
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms22

Software

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