X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GZFPDB ENTRY 1GZF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
122.5% PEG 3350 W/W, 100 MM LI2SO4, 100 MM SODIUM CITRATE PH 3.0, 3-10% MPEG 550 V/V
Crystal Properties
Matthews coefficientSolvent content
2.6853.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.837α = 90
b = 70.381β = 97.28
c = 114.688γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-3ESRFID14-3

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
12.529.8890.80.0516.94224162

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 1GZF2.529.882124411451000.2370.2320.316RANDOM46.46
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]
7.421.5-2.4-4.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.596
r_scangle_it2.916
r_scbond_it1.754
r_angle_refined_deg1.56
r_mcangle_it1.35
r_angle_other_deg0.855
r_mcbond_it0.726
r_nbd_other0.233
r_symmetry_hbond_refined0.228
r_nbd_refined0.216
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.596
r_scangle_it2.916
r_scbond_it1.754
r_angle_refined_deg1.56
r_mcangle_it1.35
r_angle_other_deg0.855
r_mcbond_it0.726
r_nbd_other0.233
r_symmetry_hbond_refined0.228
r_nbd_refined0.216
r_xyhbond_nbd_refined0.186
r_symmetry_vdw_other0.15
r_symmetry_vdw_refined0.121
r_nbtor_other0.087
r_chiral_restr0.084
r_bond_refined_d0.017
r_gen_planes_refined0.005
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 Atoms4704
Nucleic Acid Atoms
Solvent Atoms30
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing