X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.57
Temperature 293.0
Details NANODROP, 1.545M Ammonium dihydrogen phosphate, 0.1M Tris-HCl pH 8.57, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 81.89 α = 90
b = 81.89 β = 90
c = 70.63 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r 1m long Rh coated bent cylindrical mirror for horizontal and vertical focusing 2008-02-10
Diffraction Radiation
Monochromator Protocol
Double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL1-5 0.978835 SSRL BL1-5

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.7 26.8 100.0 0.097 0.097 -- 10.4 -- 30482 -- -- 19.728
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.7 1.74 100.0 0.812 0.812 0.9 7.6 2149

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
SAD 1.7 26.803 -- 0.0 -- 30438 1538 99.96 -- 0.145 0.144 0.164 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.7 1.745 -- 111 2116 0.221 0.269 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.065
Anisotropic B[1][1] 0.5
Anisotropic B[1][2] 0.25
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.5
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.74
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.085
r_nbd_other 0.206
r_nbtor_refined 0.173
r_dihedral_angle_1_deg 6.039
r_mcangle_it 3.236
r_gen_planes_refined 0.007
r_symmetry_vdw_refined 0.193
r_bond_refined_d 0.016
r_dihedral_angle_2_deg 38.518
r_symmetry_vdw_other 0.235
r_dihedral_angle_3_deg 12.489
r_scangle_it 8.068
r_angle_refined_deg 1.59
r_nbd_refined 0.264
r_scbond_it 5.832
r_mcbond_other 0.518
r_angle_other_deg 0.932
r_gen_planes_other 0.002
r_nbtor_other 0.086
r_mcbond_it 2.658
r_dihedral_angle_4_deg 9.965
r_symmetry_hbond_refined 0.186
r_bond_other_d 0.002
r_xyhbond_nbd_refined 0.232
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1145
Nucleic Acid Atoms 0
Heterogen Atoms 53
Solvent Atoms 138

Software

Software
Software Name Purpose
MolProbity model building version: 3beta29
PHENIX refinement
SHELX phasing
REFMAC refinement version: 5.2.0019
SCALA data scaling
PDB_EXTRACT data extraction version: 3.000
ADSC data collection version: Quantum
MOSFLM data reduction
SHELXD phasing
autoSHARP phasing