X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 8.5
Details CRYSTALS WERE GROWN FROM A SOLUTION CONTAINING 3.5 MG/ML PROTEIN, 30-35 % PEG 4000 10 MM ARABINOSE-5-PHOSPHATE, 0.05M TRIS-HCL PH 8.4, 0.1 M MGCL2

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.05 α = 90.23
b = 42.4 β = 100.98
c = 60.19 γ = 98.98
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC GE(220),HORIZONTAL FOCUSING MULTILAYER 2002-07-13
Diffraction Radiation
Monochromator Protocol
DIAMOND (111), GE(220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-1 -- ESRF ID14-1

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
1.25 40 81.8 -- 0.095 -- 4.3 -- 90067 -- -- --
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)
1.25 1.32 40.1 -- 0.76 1.1 3.6 --

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 1.25 40.0 -- -- -- 86708 4498 81.8 -- 0.224 0.224 0.24 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 1.25 1.28 -- 136 2767 0.304 0.293 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 10.26
Anisotropic B[1][1] -0.54
Anisotropic B[1][2] -0.68
Anisotropic B[1][3] 0.25
Anisotropic B[2][2] -0.48
Anisotropic B[2][3] -0.3
Anisotropic B[3][3] 0.89
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.122
r_scbond_it 2.236
r_mcangle_it 1.147
r_mcbond_it 0.775
r_nbd_refined 0.22
r_gen_planes_refined 0.008
r_chiral_restr 0.108
r_angle_other_deg 1.863
r_bond_refined_d 0.016
r_xyhbond_nbd_refined 0.116
r_symmetry_vdw_refined 0.161
r_symmetry_hbond_refined 0.507
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2771
Nucleic Acid Atoms 0
Heterogen Atoms 28
Solvent Atoms 159

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.0 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement
MOLREP model building