X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.3
Temperature 291.0
Details PEG 3350, PEG 400, Tris, NaCl, glycerol, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 47.03 α = 90
b = 146.64 β = 90
c = 178.49 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 -- --
Diffraction Radiation
Monochromator Protocol
Double crystal, Si(111) or Si(311) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 1.0 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 45 95.4 -- 0.057 -- -- 69924 69924 3.0 3.0 --
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 71.0 -- 0.336 3.0 -- --

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
MOLECULAR REPLACEMENT 2.1 45.64 -- 1.0 66288 66288 3570 100.0 -- 0.21742 0.21435 0.27467 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 2.174 -- 262 4934 0.242 0.311 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 25.107
Anisotropic B[1][1] 0.09
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.09
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.267
r_gen_planes_refined 0.003
r_chiral_restr 0.075
r_dihedral_angle_2_deg 17.375
r_dihedral_angle_1_deg 3.25
r_angle_refined_deg 1.122
r_bond_refined_d 0.006
r_xyhbond_nbd_refined 0.185
r_symmetry_vdw_refined 0.392
r_symmetry_hbond_refined 1.106
r_mcbond_it 5.364
r_mcangle_it 6.887
r_scbond_it 11.17
r_scangle_it 14.165
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8025
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 641

Software

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