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_scangle_it 4.179
r_scbond_it 2.515
r_mcangle_it 1.416
r_mcbond_it 0.759
r_gen_planes_refined 0.007
r_chiral_restr 0.113
r_dihedral_angle_4_deg 8.866
r_dihedral_angle_3_deg 18.141
r_dihedral_angle_2_deg 40.588
r_dihedral_angle_1_deg 6.14
r_angle_refined_deg 1.667
r_bond_refined_d 0.017
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

Computing
Computing Package Purpose
StructureStudio Data Collection
XDS Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.5.0109 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 version: 5.5.0109 refinement
MOLREP molecular replacement
SCALA version: 3.3.9 data reduction