X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.5
Temperature 298.0
Details 1.4 M Sodium Formate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.27 α = 90
b = 59.27 β = 90
c = 200.09 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 MARMOSAIC 300 mm CCD -- 2010-11-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID 1 APS 22-ID

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
2.05 50 91.7 0.09 -- -- 4.7 -- 22657 -- -- --
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)
2.07 2.14 72.8 0.562 -- -- 1.7 1779

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 2.05 25.0 -- 0.0 -- 22654 1158 91.75 -- 0.2453 0.2434 0.2787 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 2.054 2.164 -- 126 2460 0.457 0.47 -- 72.72
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 50.2723
Anisotropic B[1][1] 1.92
Anisotropic B[1][2] 0.96
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.92
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.87
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 9.121
r_scbond_it 6.522
r_mcangle_it 5.467
r_bond_refined_d 0.018
r_bond_other_d 0.067
r_angle_refined_deg 1.724
r_angle_other_deg 5.178
r_dihedral_angle_1_deg 7.587
r_dihedral_angle_2_deg 34.187
r_dihedral_angle_3_deg 21.51
r_dihedral_angle_4_deg 8.701
r_chiral_restr 0.11
r_gen_planes_refined 0.008
r_mcbond_it 3.553
r_mcbond_other 0.033
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2224
Nucleic Acid Atoms 0
Heterogen Atoms 44
Solvent Atoms 49

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL Data Reduction (intensity integration)
HKL Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.5.0102 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 version: 5.5.0102 refinement
Phaser molecular replacement
HKL data reduction