X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7
Details HANGING DROP, RESERVOIR: 10%W/V PEG 6K, 2 M NACL, PH 7.0

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 78.09 α = 90
b = 78.09 β = 90
c = 78.09 γ = 90
Symmetry
Space Group P 41 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 114
Diffraction Detector
Detector Diffraction Type Details Collection Date
-- -- -- 2003-07-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 -- -- --

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
2.07 34.92 97.7 0.055 -- -- 3.7 -- 5365 -- 2.0 --
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)
2.07 2.14 100.0 0.361 -- 1.6 3.32 --

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 2.14 55.05 -- -- -- 4579 224 98.6 -- -- 0.241 0.302 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 2.14 2.2 -- 20 332 0.269 0.403 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 50.48
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 10.393
r_scbond_it 7.164
r_mcangle_it 5.309
r_mcbond_it 3.108
r_nbd_refined 0.273
r_gen_planes_other 0.051
r_gen_planes_refined 0.037
r_chiral_restr 0.438
r_dihedral_angle_1_deg 10.159
r_angle_other_deg 2.342
r_angle_refined_deg 4.791
r_bond_other_d 0.004
r_bond_refined_d 0.075
r_nbd_other 0.265
r_nbtor_other 0.133
r_xyhbond_nbd_refined 0.192
r_symmetry_vdw_refined 0.506
r_symmetry_vdw_other 0.318
r_symmetry_hbond_refined 0.045
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 420
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 4

Software

Computing
Computing Package Purpose
CRYSTALCLEAR (MSC/RIGAKU) Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement
MOLREP model building