X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 295.0
Details 0.3-1.0M sodium chloride in the pH range 5.5-7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.53 α = 90
b = 45.53 β = 90
c = 101.93 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 298
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS HTC HighRes2 mirror system 2004-03-11
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-D 1.5418 -- --

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
1.71 27.23 -- -- 0.06 -- 5.8 -- 11367 -- -- --
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)
1.71 1.8 100.0 -- 0.368 2.5 3.0 1108

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 1.71 27.23 -- -- -- 10805 542 92.71 -- 0.19646 0.19508 0.22337 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 1.71 1.754 -- 22 489 0.362 0.486 -- 57.42
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.479
Anisotropic B[1][1] 0.37
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.37
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.75
RMS Deviations
Key Refinement Restraint Deviation
r_xyhbond_nbd_refined 0.144
r_scbond_it 2.296
r_mcbond_it 0.966
r_symmetry_vdw_refined 0.204
r_dihedral_angle_1_deg 6.36
r_chiral_restr 0.08
r_nbd_refined 0.205
r_symmetry_hbond_refined 0.3
r_bond_refined_d 0.013
r_angle_refined_deg 1.378
r_gen_planes_refined 0.005
r_scangle_it 3.927
r_dihedral_angle_2_deg 41.998
r_dihedral_angle_3_deg 13.159
r_nbtor_refined 0.307
r_dihedral_angle_4_deg 13.09
r_mcangle_it 1.455
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 756
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 114

Software

Software
Software Name Purpose
CrystalClear data collection
MOLREP phasing
REFMAC refinement version: 5.2.0019
MOSFLM data reduction
SCALA data scaling