X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 289.0
Details Cacodylate, Calcium chloride, MPD, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 65.71 α = 90
b = 69.58 β = 90
c = 75.34 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 -- 2002-06-09
Diffraction Radiation
Monochromator Protocol
-- MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-1 0.934, 0.9500, 0.9791, 0.9794 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
1.7 30 99.9 0.077 -- -- -- 39543 38674 2.0 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)
1.7 1.76 100.0 0.217 -- -- -- --

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
MAD 1.7 29.75 -- 0.0 39543 36644 1982 99.88 -- 0.18998 0.18791 0.22863 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 1.7 1.744 -- 134 2671 0.21 0.243 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.529
Anisotropic B[1][1] -1.45
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.54
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.09
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 5.771
r_sphericity_free 22.5
r_rigid_bond_restr 1.013
r_scangle_it 4.304
r_scbond_it 2.79
r_mcangle_it 1.775
r_bond_refined_d 0.01
r_angle_refined_deg 1.205
r_dihedral_angle_1_deg 3.053
r_dihedral_angle_3_deg 14.888
r_chiral_restr 0.095
r_gen_planes_refined 0.004
r_nbd_refined 0.237
r_xyhbond_nbd_refined 0.163
r_metal_ion_refined 0.118
r_symmetry_vdw_refined 0.332
r_symmetry_hbond_refined 0.654
r_mcbond_it 1.017
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2680
Nucleic Acid Atoms 0
Heterogen Atoms 8
Solvent Atoms 234

Software

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