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 CCD 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_gen_planes_other 0.003
r_angle_other_deg 2.009
r_symmetry_hbond_refined 0.224
r_dihedral_angle_3_deg 18.757
r_chiral_restr 0.105
r_xyhbond_nbd_refined 0.133
r_bond_refined_d 0.014
r_symmetry_vdw_other 0.301
r_gen_planes_refined 0.006
r_dihedral_angle_1_deg 5.001
r_symmetry_vdw_refined 0.358
r_mcangle_it 1.466
r_angle_refined_deg 1.573
r_nbd_other 0.216
r_xyhbond_nbd_other 0.1
r_nbd_refined 0.244
r_nbtor_other 0.655
r_mcbond_it 0.837
r_scbond_it 2.206
r_bond_other_d 0.002
r_scangle_it 3.508
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

Software
Software Name Purpose
REFMAC refinement version: 5.0
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing