X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Evaporation
pH 5.5
Temperature 293.0
Details MPD, TRIS, acetate, NaCl, Lysine, pH 5.5, EVAPORATION, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 140.5 α = 90
b = 108.89 β = 90
c = 50.42 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2002-06-27
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1

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
1.3 50.77 85.9 0.059 -- -- 5.5 190258 163406 -- 3.0 18.62
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)
1.3 1.35 72.6 0.064 -- -- 2.5 13256

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 1.3 50.77 -- 0.0 162173 155206 8200 85.89 -- 0.14596 0.14499 0.16494 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 1.3 1.334 -- 532 9366 0.216 0.228 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 11.354
Anisotropic B[1][1] -0.5
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.03
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.53
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_other 0.083
r_nbd_other 0.253
r_nbd_refined 0.224
r_gen_planes_other 0.012
r_gen_planes_refined 0.008
r_chiral_restr 0.083
r_dihedral_angle_1_deg 5.611
r_angle_other_deg 0.83
r_angle_refined_deg 1.399
r_bond_other_d 0.002
r_bond_refined_d 0.01
r_xyhbond_nbd_refined 0.168
r_symmetry_vdw_refined 0.19
r_symmetry_vdw_other 0.271
r_symmetry_hbond_refined 0.18
r_mcbond_it 0.691
r_mcangle_it 1.263
r_scbond_it 1.926
r_scangle_it 3.092
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5751
Nucleic Acid Atoms 0
Heterogen Atoms 96
Solvent Atoms 924

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (SCALA, TRUNCATE) Data Reduction (data scaling)
T-COFFEE, MODELLER, AMORE Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement