X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.5
Details HANGING DROP EXPERIMENT RESERVOIR: 13% PEG MME 5K, 0.5M LICL, 10% ISOPROPANOL, 0.1M HEPES PH 7.5, 5MM DTT, 1MM UDP-TRIPEPTIDE DROP: 2UL PROTEIN SOLUTION (MURE @ 10MGML-1 IN 20MM HEPES PH 7.5, 200MM NACL, 5MM DTT) WITH 2UL RESERVOIR SOLUTION.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 93.46 α = 90
b = 99.69 β = 90
c = 236.15 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 1999-11-15
Diffraction Radiation
Monochromator Protocol
GE MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE BM14 0.9791,0.9790,0.8550,0.93 ESRF BM14

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 46.7 98.3 -- 0.066 -- 4.5 -- 323548 -- -- 19.3
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)
2.0 2.13 91.2 -- 0.22 -- 3.9 --

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
MAD 2.0 46.73 -- 0.0 -- 72674 7348 98.0 -- 0.202 0.202 0.23 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 2.0 2.13 -- 1080 9702 0.214 0.25 0.008 87.5
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 34.4
Anisotropic B[1][1] 1.81
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.95
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.87
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.006
c_improper_angle_d 0.78
c_angle_deg 1.3
c_dihedral_angle_d 23.5
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.22
Luzzati Sigma A (Observed) 0.12
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.27
Luzzati Sigma A (R-Free Set) 0.18
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7528
Nucleic Acid Atoms 0
Heterogen Atoms 141
Solvent Atoms 393

Software

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