X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1UYPPDB ENTRY 1UYP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.2293HANGING DROP TECHNIQUE 10% PEG 1000, 50 MM LI2SO4, 100 MM CITRATE PHOSPHATE BUFFER PH 4.2, CONCENTRATION PROTEIN 8 MG/ML, INCUBATION TEMPERATURE 20 C
Crystal Properties
Matthews coefficientSolvent content
2.244

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.5α = 90
b = 114.7β = 98.9
c = 130γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray294CCDADSC CCDMIRRORS2004-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
11.87129.09997.70.06263.3225700
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)
11.873097.80.1843.93

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 1UYP1.87402093871105597.70.1990.1980.229RANDOM15.8
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]
0.911.14-0.640.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.484
r_scangle_it1.729
r_angle_refined_deg1.103
r_scbond_it1.044
r_angle_other_deg0.854
r_mcangle_it0.792
r_symmetry_hbond_refined0.5
r_mcbond_it0.413
r_symmetry_vdw_refined0.293
r_nbd_other0.233
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.484
r_scangle_it1.729
r_angle_refined_deg1.103
r_scbond_it1.044
r_angle_other_deg0.854
r_mcangle_it0.792
r_symmetry_hbond_refined0.5
r_mcbond_it0.413
r_symmetry_vdw_refined0.293
r_nbd_other0.233
r_symmetry_vdw_other0.222
r_nbd_refined0.183
r_xyhbond_nbd_refined0.136
r_nbtor_other0.085
r_chiral_restr0.074
r_bond_refined_d0.006
r_gen_planes_refined0.003
r_gen_planes_other0.003
r_bond_other_d0.002
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_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms21109
Nucleic Acid Atoms
Solvent Atoms1888
Heterogen Atoms237

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALAdata scaling