X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4A3QPDB ENTRY 4A3Q

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.529820 mg/ml protein in 50mM Tris pH 8.0, 0.02% v/v BME, 10 micromolar pyridoxal-L-phosphate, crystallization buffer 1mM TCEP, 0.2M sodium formate, 20% w/V PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4449.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.15α = 90
b = 93.3β = 91
c = 107.09γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS HTC2012-09-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT

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
12.07654.5488.40.0619.57.5932512
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)
12.0762.252.90.3744.97

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 4A3Q2.154.5488493455595.110.204780.201560.26571RANDOM39.958
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]
-0.04-0.270.04-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.591
r_dihedral_angle_4_deg21.082
r_long_range_B_refined7.174
r_mcangle_it5.083
r_scbond_it4.655
r_mcbond_it3.792
r_angle_refined_deg2.014
r_chiral_restr0.127
r_bond_refined_d0.018
r_gen_planes_refined0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.591
r_dihedral_angle_4_deg21.082
r_long_range_B_refined7.174
r_mcangle_it5.083
r_scbond_it4.655
r_mcbond_it3.792
r_angle_refined_deg2.014
r_chiral_restr0.127
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_1_deg
r_dihedral_angle_3_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
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 Atoms11888
Nucleic Acid Atoms
Solvent Atoms568
Heterogen Atoms22

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling