X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 4.6
Details PROTEIN WAS CONCENTRATED TO 20 MG/ML IN WATER. CRYSTALLISATION IN 200MM MAGNESIUM ACETATE IN 100MM SODIUM ACETATE BUFFER AT PH 4.6. PRECIPITANT WAS 20%. POLYETHYLENE GLYCOL 5500.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.26 α = 90
b = 68.38 β = 112.39
c = 55.18 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
CCD ADSC TORROIDAL MIRROR 2001-10-15
Diffraction Radiation
Monochromator Protocol
DIAMOND (111), GE(220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-2 -- ESRF ID14-2

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 99.1 0.062 -- -- 3.8 -- 26197 -- 0.0 --
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)
1.9 1.93 98.0 0.28 -- 4.6 3.7 --

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 1.9 30.0 -- -- -- 24685 1324 99.2 -- 0.168 0.166 0.211 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 1.9 1.95 -- 90 1803 0.194 0.245 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.18
Anisotropic B[1][1] -0.8
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.06
Anisotropic B[2][2] -0.71
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.7
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.508
r_scbond_it 2.206
r_mcangle_it 1.466
r_mcbond_it 0.837
r_nbd_refined 0.244
r_gen_planes_other 0.003
r_gen_planes_refined 0.006
r_chiral_restr 0.105
r_dihedral_angle_3_deg 18.757
r_dihedral_angle_1_deg 5.001
r_angle_other_deg 2.009
r_angle_refined_deg 1.573
r_bond_other_d 0.002
r_bond_refined_d 0.014
r_nbd_other 0.216
r_nbtor_other 0.655
r_xyhbond_nbd_refined 0.133
r_xyhbond_nbd_other 0.1
r_symmetry_vdw_refined 0.358
r_symmetry_vdw_other 0.301
r_symmetry_hbond_refined 0.224
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2821
Nucleic Acid Atoms 0
Heterogen Atoms 62
Solvent Atoms 270

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5.0 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement
AMORE model building