X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 293.0
Details PEG, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 65.5 α = 90
b = 68.24 β = 90
c = 419.29 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 90
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 mirrors 2001-11-04
Diffraction Radiation
Monochromator Protocol
mirror MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 0.9765 ESRF ID14-4

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 12 82.9 -- -- -- -- 234528 87113 0.0 0.0 --
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)
2.1 2.2 72.3 0.268 -- -- -- --

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 2.1 12.0 -- 0.0 87113 87113 4619 82.99 0.2174 0.21747 0.21485 0.2656 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 2.1 2.153 -- 91 2014 0.246 0.278 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 32.635
Anisotropic B[1][1] -2.3
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 4.24
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.93
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.638
r_scbond_it 2.3
r_mcangle_it 1.603
r_mcbond_it 0.874
r_symmetry_hbond_refined 0.397
r_symmetry_vdw_other 0.277
r_symmetry_vdw_refined 0.235
r_xyhbond_nbd_other 0.115
r_xyhbond_nbd_refined 0.155
r_bond_refined_d 0.018
r_bond_other_d 0.001
r_angle_refined_deg 1.867
r_angle_other_deg 0.889
r_dihedral_angle_1_deg 5.183
r_dihedral_angle_2_deg 19.35
r_chiral_restr 0.135
r_gen_planes_refined 0.007
r_gen_planes_other 0.004
r_nbd_refined 0.24
r_nbd_other 0.223
r_nbtor_other 0.494
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 11926
Nucleic Acid Atoms 0
Heterogen Atoms 118
Solvent Atoms 322

Software

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