X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 290.0
Details 10mM Tris-HCl, 250mM NaCl, 5mM DTT, 50mM calcium acetate, 18% PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 64.97 α = 90
b = 66.85 β = 90
c = 110.79 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 -- 2007-09-13
Diffraction Radiation
Monochromator Protocol
Diamond(111),Ge(220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2

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
2.9 50 99.7 0.081 -- -- 7.0 11166 11166 -- -- 65.993
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)
2.9 3.0 100.0 0.317 -- -- 7.2 1094

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
-- 2.9 10.0 -- 0.0 -- 10834 512 99.58 0.221 0.221 0.217 0.289 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 2.899 2.968 -- 42 662 0.318 0.349 -- 95.14
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 48.367
Anisotropic B[1][1] 5.37
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.6
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.77
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 4.309
r_mcangle_it 0.502
r_scbond_it 0.552
r_scangle_it 0.88
r_xyhbond_nbd_refined 0.128
r_dihedral_angle_3_deg 15.385
r_angle_refined_deg 1.043
r_dihedral_angle_2_deg 38.676
r_mcbond_it 0.268
r_symmetry_hbond_refined 0.049
r_chiral_restr 0.069
r_nbd_refined 0.178
r_bond_refined_d 0.006
r_symmetry_vdw_refined 0.166
r_dihedral_angle_4_deg 23.301
r_gen_planes_refined 0.003
r_nbtor_refined 0.293
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3601
Nucleic Acid Atoms 0
Heterogen Atoms 54
Solvent Atoms 26

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
REFMAC refinement version: 5.2.0019
PDB_EXTRACT data extraction version: 3.006
HKL-2000 data reduction
HKL-2000 data scaling
AMoRE phasing