X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.6
Temperature 295.0
Details Protein: 20.0mG/mL, 0.5M Sodium chloride, 0.01M Tris-HCl (pH 8.3); Screen: PEG's (A2), 0.1M Sodium acetate (pH 4.6), 30% (v/v) PEG 300, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 64.4 α = 90
b = 64.4 β = 90
c = 591.61 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 300 mm CCD Mirrors 2011-10-06
Diffraction Radiation
Monochromator Protocol
Si {1,1,1} SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-D 0.97903 APS 21-ID-D

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
1.85 30 99.4 0.088 -- -- 14.3 64336 64336 -- -3.0 23.6
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)
1.85 1.88 99.3 0.606 -- 5.3 15.0 3115

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 1.85 29.52 -- -- 61040 61040 3242 99.6 0.1558 0.1558 0.15425 0.18465 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 1.85 1.898 4335 229 4335 0.191 0.253 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Thermal Factors Individually Refined
Mean Isotropic B 20.557
Anisotropic B[1][1] 0.59
Anisotropic B[1][2] 0.29
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.59
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.88
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.359
r_scbond_it 2.715
r_mcangle_it 1.676
r_mcbond_other 0.304
r_bond_refined_d 0.011
r_bond_other_d 0.001
r_angle_refined_deg 1.323
r_angle_other_deg 0.83
r_dihedral_angle_1_deg 3.278
r_dihedral_angle_2_deg 33.954
r_dihedral_angle_3_deg 9.449
r_dihedral_angle_4_deg 12.809
r_chiral_restr 0.087
r_gen_planes_refined 0.006
r_gen_planes_other 0.002
r_mcbond_it 0.966
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4828
Nucleic Acid Atoms 0
Heterogen Atoms 32
Solvent Atoms 540

Software

Computing
Computing Package Purpose
Blu Max Data Collection
HKL-3000 Data Reduction (intensity integration)
HKL-3000 Data Reduction (data scaling)
PHENIX Structure Solution
REFMAC 5.5.0102 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0102 refinement
PHENIX model building
Blu version: Max data collection