X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 4.6
Details PROTEIN WAS CONCENTRATED TO 10 MG/ML IN WATER. CRYSTALLISATION IN 200MM MAGNESIUM ACETATE IN 100MM SODIUM ACETATE BUFFER AT PH 4.6. PRECIPITANT WAS 20% POLYETHYLENE GLYCOL 5K MME.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 47.44 α = 90
b = 67.55 β = 110.87
c = 53.66 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 2002-06-15
Diffraction Radiation
Monochromator Protocol
DIAMOND (111), GE(220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-1 -- 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
1.3 30 90.0 0.068 -- -- 3.6 -- 79327 -- 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)
1.3 1.35 52.3 0.27 -- 4.6 1.6 --

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 1.3 30.0 -- -- -- 67142 3548 91.0 -- 0.146 0.145 0.174 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 1.3 1.33 -- 146 2974 0.21 0.252 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 12.36
Anisotropic B[1][1] -0.59
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.03
Anisotropic B[2][2] 0.16
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.41
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_hbond_refined 0.152
r_mcangle_it 2.051
r_bond_refined_d 0.015
r_dihedral_angle_1_deg 6.037
r_mcbond_it 1.377
r_gen_planes_other 0.01
r_chiral_restr 0.146
r_bond_other_d 0.002
r_angle_refined_deg 1.701
r_symmetry_vdw_refined 0.145
r_angle_other_deg 0.969
r_gen_planes_refined 0.016
r_scbond_it 2.669
r_nbd_other 0.249
r_symmetry_vdw_other 0.258
r_xyhbond_nbd_refined 0.122
r_scangle_it 3.844
r_nbd_refined 0.231
r_nbtor_other 0.085
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2804
Nucleic Acid Atoms 0
Heterogen Atoms 76
Solvent Atoms 402

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.24
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing