X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.1
Temperature 293.0
Details PEG3350, citric acid, Bis-Tris propane, pH 4.1, vapor diffusion, hanging drop, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 153.35 α = 90
b = 114.16 β = 95.62
c = 68.34 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ Osmic Blue 2008-06-23
Diffraction Radiation
Monochromator Protocol
Osmic Blue SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 1.54 -- --

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
2.2 50 99.1 0.106 -- -- 6.0 -- 59205 -- -- 54.3
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)
2.2 2.28 95.9 0.674 -- 2.0 4.2 5733

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
FOURIER SYNTHESIS 2.2 39.01 -- 0.0 -- 59203 2984 98.66 -- 0.167 0.165 0.205 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 2.2 2.249 -- 195 3775 0.295 0.342 -- 90.21
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 36.6
Anisotropic B[1][1] -0.06
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.01
Anisotropic B[2][2] -0.07
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.13
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.833
r_scbond_it 3.42
r_mcangle_it 3.55
r_mcbond_it 2.503
r_gen_planes_refined 0.004
r_chiral_restr 0.074
r_dihedral_angle_4_deg 18.783
r_dihedral_angle_3_deg 13.709
r_dihedral_angle_2_deg 34.48
r_dihedral_angle_1_deg 5.732
r_angle_refined_deg 1.109
r_bond_refined_d 0.007
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.189
Luzzati ESD (R-Free Set) 0.164
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6162
Nucleic Acid Atoms 0
Heterogen Atoms 357
Solvent Atoms 655

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
REFMAC 5.5.0070 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.005 data extraction
REFMAC5 version: 5.5.0070 refinement
HKL data processing