X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4
Temperature 293.2
Details PEG6000, sodium citrate, calcium chloride, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.2K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 65.48 α = 90
b = 58.69 β = 109.62
c = 67.04 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2000-10-10
CCD ADSC QUANTUM 4 -- 2000-05-18
Diffraction Radiation
Monochromator Protocol
a fixed-exit double crystal monochromator SINGLE WAVELENGTH
Si 111 channel SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL44B2 1.0000 SPRING-8 BL44B2
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 1.0000 PHOTON FACTORY BL-6A

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
1.9 30 98.2 0.065 0.055 -- 5.1 37943 37256 3.0 3.0 19.4
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)
1.9 2.0 98.4 0.176 0.15 4.6 3.6 5352

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
MIR 1.9 20.0 0.0 0.0 37904 37184 1852 98.1 -- -- 0.194 0.222 RANDOM
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC
Mean Isotropic B 21.1
Anisotropic B[1][1] 2.228
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.737
Anisotropic B[2][2] 1.374
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.602
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 0.85
c_dihedral_angle_d 21.2
c_angle_deg 1.254
c_bond_d 0.005
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.21
Luzzati Sigma A (Observed) 0.12
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.24
Luzzati Sigma A (R-Free Set) 0.16
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3524
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 315

Software

Computing
Computing Package Purpose
MOSFLM, DENZO Data Reduction (intensity integration)
CCP4 (SCALA), SCALEPACK Data Reduction (data scaling)
MLPHARE, DM Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement
DM model building
MLPHARE model building
SCALEPACK data reduction
SCALA data reduction
DENZO data collection
MOSFLM data collection