X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 277.0
Details 2.6 M ammonium sulfate, 0.1 M sodium phosphate buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 29.19 α = 90
b = 46.4 β = 90
c = 56.81 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 MAR CCD 165 mm MIRRORS 2002-03-04
Diffraction Radiation
Monochromator Protocol
double crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 1.05 MPG/DESY, HAMBURG BW6

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 15.94 97.1 0.048 -- -- 3.2 42532 41299 -- 2.0 5.52
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)
1.0 1.02 88.2 0.271 -- 3.0 2.5 2087

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 1.0 15.94 -- -- 40302 39177 2080 97.21 -- 0.11771 0.11673 0.13629 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 1.0 1.026 2643 141 2643 0.243 0.286 -- 91.34
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ANISOTROPIC
Mean Isotropic B 10.2
Anisotropic B[1][1] 0.02
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] -0.02
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 5.999
r_sphericity_free 15.633
r_rigid_bond_restr 2.75
r_scangle_it 7.116
r_scbond_it 5.188
r_mcangle_it 3.228
r_mcbond_it 2.468
r_nbd_refined 0.442
r_gen_planes_refined 0.012
r_chiral_restr 0.154
r_dihedral_angle_3_deg 12.087
r_dihedral_angle_2_deg 29.515
r_dihedral_angle_1_deg 7.187
r_angle_refined_deg 2.415
r_bond_refined_d 0.025
r_nbtor_refined 0.324
r_xyhbond_nbd_refined 0.505
r_metal_ion_refined 0.041
r_symmetry_vdw_refined 0.221
r_symmetry_hbond_refined 0.328
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 738
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 228

Software

Computing
Computing Package Purpose
Marccd Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
Molrep Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0019 refinement
Molrep model building
Marccd data collection