X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 298.0
Details PEG 8000, potassium thiocyanate, L-proline, glycerol, hexanediol, CHAPS, lutetium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 70.3 α = 90
b = 119.1 β = 90
c = 158.7 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 1999-10-05
Diffraction Radiation
Monochromator Protocol
Si 111 Channel SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-BM-C 0.98 APS 14-BM-C

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
2.5 40 91.4 0.039 0.039 -- 2.9 42943 42943 -3.0 -3.0 54.0
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)
2.5 2.64 82.4 0.254 0.254 2.7 2.6 5587

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 2.5 34.5 0.0 0.0 42943 41361 1306 88.0 0.22 0.21819 0.21676 0.26535 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 2.5 2.565 2615 85 2615 0.257 0.367 -- 76.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 30.167
Anisotropic B[1][1] 1.89
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.66
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.22
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.222
r_gen_planes_refined 0.004
r_chiral_restr 0.092
r_dihedral_angle_3_deg 19.868
r_dihedral_angle_1_deg 3.289
r_angle_refined_deg 1.335
r_bond_refined_d 0.009
r_xyhbond_nbd_refined 0.156
r_symmetry_vdw_refined 0.194
r_symmetry_hbond_refined 0.166
r_mcbond_it 1.505
r_mcangle_it 2.642
r_scbond_it 3.916
r_scangle_it 5.698
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7776
Nucleic Acid Atoms 0
Heterogen Atoms 2
Solvent Atoms 161

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement
CNS model building