X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Temperature 273.0
Details 4.0M NaFormate, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 273K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 115.98 α = 90
b = 115.98 β = 90
c = 119.64 γ = 120
Symmetry
Space Group P 65 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 Double-crystal monochromator (Si 111), toroid 2005-05-05
Diffraction Radiation
Monochromator Protocol
-- MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL1-5 0.979094, 0.918381 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
2.1 29.91 99.9 0.088 0.088 -- 6.8 -- 28282 -- -- --
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)
2.1 2.15 -- 0.766 0.766 1.0 4.2 --

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
MAD 2.15 29.2 -- -- -- 25047 1332 99.87 0.18 -- 0.177 0.228 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 2.15 2.206 -- 97 1808 0.229 0.295 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 38.566
Anisotropic B[1][1] -1.33
Anisotropic B[1][2] -0.66
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.33
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.99
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.001
r_gen_planes_refined 0.006
r_chiral_restr 0.084
r_nbd_refined 0.21
r_dihedral_angle_4_deg 15.613
r_xyhbond_nbd_refined 0.143
r_mcangle_it 3.226
r_bond_other_d 0.001
r_nbtor_refined 0.181
r_angle_other_deg 0.781
r_mcbond_other 0.529
r_scangle_it 7.474
r_symmetry_hbond_refined 0.232
r_bond_refined_d 0.016
r_dihedral_angle_1_deg 5.56
r_dihedral_angle_2_deg 35.444
r_nbd_other 0.173
r_dihedral_angle_3_deg 12.987
r_nbtor_other 0.085
r_scbond_it 5.604
r_mcbond_it 2.395
r_symmetry_vdw_other 0.24
r_angle_refined_deg 1.406
r_symmetry_vdw_refined 0.179
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1863
Nucleic Acid Atoms 0
Heterogen Atoms 42
Solvent Atoms 187

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
SCALA data scaling
PDB_EXTRACT data extraction version: 1.601
MOSFLM data reduction
CCP4 data scaling version: (SCALA)
SOLVE phasing