X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.8
Temperature 298.0
Details 0.15M Calcium chloride dihydrate, 0.1M HEPES-Na, 20% (w/v)Polyethylene glycol 2000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.14 α = 90
b = 74.75 β = 95.72
c = 58.67 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ Varimax mirror 2010-12-08
Diffraction Radiation
Monochromator Protocol
Varimax optics SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF 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
2.3 58.37 97.6 -- 0.094 -- 3.7 16871 16871 2.0 2.0 --
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)
2.3 2.42 95.9 0.235 0.235 3.2 3.6 2401

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 2.3 58.37 -- 0.0 -- 16852 850 97.21 -- 0.1769 0.1724 0.2636 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 2.3 2.36 -- 52 1149 0.169 0.248 -- 94.72
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.703
Anisotropic B[1][1] -0.89
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.42
Anisotropic B[2][2] 0.6
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.21
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 6.14
r_gen_planes_refined 0.007
r_dihedral_angle_4_deg 8.866
r_mcbond_it 0.759
r_mcangle_it 1.416
r_dihedral_angle_3_deg 18.141
r_chiral_restr 0.113
r_dihedral_angle_2_deg 40.588
r_scangle_it 4.179
r_scbond_it 2.515
r_bond_refined_d 0.017
r_angle_refined_deg 1.667
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2985
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 260

Software

Software
Software Name Purpose
SCALA data scaling version: 3.3.9
MOLREP phasing
REFMAC refinement version: 5.5.0109
PDB_EXTRACT data extraction version: 3.10
StructureStudio data collection
XDS data reduction