X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Microgravity with Apcf Reactors
pH 6.5
Temperature 295.0
Details Tris HCl, CaCl2, NaNO3, pH 6.5, microgravity with APCF reactors, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 67.83 α = 90
b = 67.83 β = 90
c = 101.56 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH mirrors 2000-10-10
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.91 EMBL/DESY, HAMBURG X11

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
1.02 20 99.0 -- 0.063 -- 15.8 119205 119205 -3.0 -3.0 5.0
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)
1.02 1.06 95.0 -- 0.234 5.58 -- 11282

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 1.02 20.0 0.0 0.0 119205 119205 1192 99.82 0.12917 0.1291 0.12904 0.14162 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 1.02 1.045 -- 91 8138 0.182 0.214 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model anisotropic
Mean Isotropic B 7.92
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.01
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 2.461
r_sphericity_free 6.967
r_rigid_bond_restr 1.095
r_scangle_it 3.736
r_scbond_it 2.486
r_mcangle_it 1.704
r_mcbond_it 1.066
r_symmetry_hbond_refined 0.409
r_symmetry_vdw_other 0.412
r_symmetry_vdw_refined 0.543
r_bond_refined_d 0.009
r_bond_other_d 0.006
r_angle_refined_deg 1.482
r_angle_other_deg 0.919
r_dihedral_angle_1_deg 6.716
r_chiral_restr 0.218
r_gen_planes_refined 0.008
r_gen_planes_other 0.003
r_nbd_refined 0.263
r_nbd_other 0.276
r_nbtor_other 0.088
r_xyhbond_nbd_refined 0.199
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.2
Luzzati Sigma A (Observed) 0.09
Luzzati Resolution Cutoff (Low) 5.0
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2077
Nucleic Acid Atoms 0
Heterogen Atoms 22
Solvent Atoms 432

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement