X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.6
Temperature 293.15
Details 35% 2-methyl-2,4-pentanediol, 0.1 M sodium acetate pH 4.6, 0.02 M CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 74.34 α = 90
b = 64.89 β = 90
c = 31.2 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm mirrors 2003-10-27
Diffraction Radiation
Monochromator Protocol
double crystal monochromator, Si-111 crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1

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
1.29 19.5 97.9 0.066 -- -- 6.3 38879 38068 -3.0 -3.0 16.166
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)
1.29 1.5 95.1 0.239 -- 6.1 6.2 13269

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 1.29 19.5 -- 0.0 38036 36128 1908 95.0 0.132 0.132 0.13 0.162 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 1.29 1.335 3577 169 3408 0.175 0.228 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Anisotropic
Mean Isotropic B 10.87
Anisotropic B[1][1] -0.37
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.25
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.62
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_vdw_other 0.309
r_sphericity_free 14.831
r_nbd_refined 0.203
r_nbd_other 0.263
r_angle_refined_deg 1.567
r_bond_other_d 0.004
r_gen_planes_refined 0.011
r_scangle_it 5.166
r_bond_refined_d 0.018
r_mcangle_it 3.158
r_symmetry_hbond_refined 0.165
r_chiral_restr 0.096
r_nbtor_other 0.086
r_symmetry_vdw_refined 0.203
r_mcbond_it 2.177
r_sphericity_bonded 6.33
r_gen_planes_other 0.013
r_rigid_bond_restr 1.479
r_angle_other_deg 0.98
r_dihedral_angle_1_deg 4.346
r_xyhbond_nbd_refined 0.135
r_scbond_it 3.878
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1117
Nucleic Acid Atoms 246
Heterogen Atoms 1
Solvent Atoms 250

Software

Software
Software Name Purpose
XSCALE data scaling
AMoRE phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 2.000
MAR345 data collection
XDS data scaling