X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 277.0
Details 17% MPD, 25 mM Potassium Phosphate, Calcium Chloride, pdTp, pH 8.0, vapor diffusion, hanging drop, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 31.1 α = 90
b = 60.65 β = 94.44
c = 36.95 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD BRUKER APEX II multi-layer optics 2007-09-05
Diffraction Radiation
Monochromator Protocol
GE111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SEALED TUBE OTHER 1.5418 -- --

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
1.8 31.5 99.37 -- 0.152 -- 13.18 -- 14206 0.0 0.0 --
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)
1.8 1.9 100.0 -- 0.415 6.22 7.86 --

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 1.8 31.01 -- -- 12767 10735 1179 93.32 -- 0.19556 0.1895 0.2512 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 1.8 1.847 -- 83 737 0.273 0.362 -- 85.15
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 22.944
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.01
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.01
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 2.535
r_xyhbond_nbd_refined 0.139
r_bond_refined_d 0.017
r_gen_planes_refined 0.006
r_dihedral_angle_2_deg 34.112
r_dihedral_angle_4_deg 9.345
r_mcbond_it 1.11
r_dihedral_angle_3_deg 16.675
r_angle_refined_deg 1.772
r_mcangle_it 1.629
r_chiral_restr 0.121
r_dihedral_angle_1_deg 5.907
r_symmetry_hbond_refined 0.135
r_scangle_it 3.785
r_nbtor_refined 0.31
r_nbd_refined 0.23
r_symmetry_vdw_refined 0.121
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1047
Nucleic Acid Atoms 0
Heterogen Atoms 26
Solvent Atoms 106

Software

Software
Software Name Purpose
SAINT data scaling
PHASER phasing
REFMAC refinement version: 5.2.0019
PDB_EXTRACT data extraction version: 3.000
APEX data collection
SAINT data reduction