X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 293.0
Details 40% PEG 300, 0.2M Calcium acetate, 0.1M Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 38.74 α = 90
b = 38.74 β = 90
c = 246.46 γ = 120
Symmetry
Space Group P 65 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2007-02-11
Diffraction Radiation
Monochromator Protocol
SI(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X10SA 0.79987 SLS X10SA

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
1.5 50 98.3 0.114 -- -- 13.8 18632 18632 0.0 0.0 18.3
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)
1.5 1.59 89.6 0.55 -- 2.8 6.6 2617

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 1.5 41.06 0.0 0.0 18632 18632 960 98.84 0.213 0.213 0.212 0.231 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 1.5 1.539 1190 67 1123 0.339 0.316 -- 89.01
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 7.375
Anisotropic B[1][1] 0.17
Anisotropic B[1][2] 0.09
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.17
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.26
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_other 0.074
r_bond_refined_d 0.005
r_nbd_other 0.174
r_gen_planes_other 0.001
r_scbond_it 0.696
r_symmetry_vdw_refined 0.169
r_mcangle_it 0.39
r_metal_ion_refined 0.104
r_nbd_refined 0.179
r_dihedral_angle_1_deg 5.118
r_xyhbond_nbd_refined 0.107
r_angle_refined_deg 0.919
r_symmetry_metal_ion_refined 0.054
r_dihedral_angle_4_deg 9.39
r_bond_other_d 0.001
r_gen_planes_refined 0.002
r_symmetry_hbond_refined 0.073
r_symmetry_vdw_other 0.213
r_angle_other_deg 0.767
r_dihedral_angle_2_deg 36.057
r_mcbond_it 0.236
r_chiral_restr 0.055
r_nbtor_refined 0.151
r_mcbond_other 0.048
r_scangle_it 1.082
r_dihedral_angle_3_deg 9.282
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 677
Nucleic Acid Atoms 0
Heterogen Atoms 26
Solvent Atoms 105

Software

Software
Software Name Purpose
PHASER phasing
REFMAC refinement version: 5.3.0034
PDB_EXTRACT data extraction version: 2.000
MAR345 data collection version: CCD
XDS data reduction
XDS data scaling