X-RAY DIFFRACTION Experimental Data & Validation


Lost? View more X-Ray Crystallographic info.

Crystallization

Crystalization Experiments
Method Precipitation
pH 8
Temperature 277.0
Details 150 mM NaCl, 40 mM Tris-HCl, 5 % w/v glycerol, 2.5 mM CaCl2, pH 8.0, precipitation, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.44 α = 90
b = 48.44 β = 90
c = 135.78 γ = 120
Symmetry
Space Group P 65

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2008-11-06
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-2 0.9330 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
2.95 41.96 100.0 0.263 0.263 -- 7.6 3840 3839 -- -- 86.0
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)
2.95 3.11 100.0 0.412 0.412 1.9 5.5 553

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 3.0 35.69 -- 0.0 -- 3615 164 100.0 -- 0.249 0.248 0.267 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 3.001 3.078 -- 17 239 0.305 0.238 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 56.744
Anisotropic B[1][1] 0.42
Anisotropic B[1][2] 0.21
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.42
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.63
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 1.264
r_scbond_it 0.803
r_mcangle_it 0.623
r_mcbond_it 0.401
r_symmetry_hbond_refined 0.35
r_bond_refined_d 0.014
r_angle_refined_deg 1.69
r_dihedral_angle_1_deg 5.971
r_dihedral_angle_2_deg 27.249
r_dihedral_angle_3_deg 24.613
r_dihedral_angle_4_deg 23.701
r_chiral_restr 0.126
r_gen_planes_refined 0.005
r_nbd_refined 0.261
r_nbtor_refined 0.326
r_xyhbond_nbd_refined 0.168
r_symmetry_vdw_refined 0.409
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1208
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 0

Software

Computing
Computing Package Purpose
MXCUBE Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.006 data extraction
REFMAC5 refinement
Phaser molecular replacement
SCALA version: 3.2.25 data processing
Mosflm collection/data indexing