X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Temperature 291.0
Details MPD, Acetate, Calcium Chloride, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 136.41 α = 90
b = 136.41 β = 90
c = 218.83 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 315 Double crystal 2007-11-21
Diffraction Radiation
Monochromator Protocol
Double crystal, Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.2.1 0.9794 ALS 8.2.1

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
2.2 50 99.9 -- 0.09 -- 6.2 -- 119629 -- -- --
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)
2.2 2.28 -- -- 0.395 5.0 6.2 2487

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
-- 2.2 40.13 -- 0.0 -- 119629 6018 99.94 -- 0.194 0.192 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 2.2 2.257 -- 456 8223 0.221 0.294 -- 99.99
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.872
Anisotropic B[1][1] -0.02
Anisotropic B[1][2] -0.01
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.02
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.03
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_refined 0.297
r_mcbond_it 0.909
r_angle_refined_deg 1.555
r_dihedral_angle_1_deg 5.672
r_bond_refined_d 0.013
r_dihedral_angle_3_deg 17.486
r_dihedral_angle_4_deg 18.114
r_dihedral_angle_2_deg 30.626
r_chiral_restr 0.09
r_nbd_refined 0.204
r_symmetry_vdw_refined 0.291
r_xyhbond_nbd_refined 0.158
r_symmetry_hbond_refined 0.23
r_scbond_it 2.116
r_mcangle_it 1.449
r_scangle_it 3.263
r_gen_planes_refined 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 10188
Nucleic Acid Atoms 2807
Heterogen Atoms 0
Solvent Atoms 466

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
REFMAC refinement
PDB_EXTRACT data extraction version: 3.004
ADSC data collection version: Quantum
HKL-2000 data reduction
HKL-2000 data scaling
AMoRE phasing