X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.5
Details PROTEIN WAS CONCENTRATED TO 10MG/ML IN WATER.CRYSTALLISATION IN 200MM CALCIUM ACETATE, 100MM HEPES PH 7.5 AND 21% POLYETHYLENE GLYCOL 5KMME.20 % GLYCEROL WAS ADDED FOR CRYOPROTECTION

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 49.36 α = 90
b = 69.84 β = 113.52
c = 51.95 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 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
1.31 15 91.7 0.06 -- -- 6.2 -- 77018 -- 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)
1.31 1.33 100.0 0.275 -- 7.6 5.6 --

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 1.31 15.0 -- -- -- 65959 3485 90.2 -- 0.132 0.13 0.162 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 1.31 1.35 -- 271 5079 0.146 0.198 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 12.29
Anisotropic B[1][1] 0.13
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.28
Anisotropic B[2][2] -0.2
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.3
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.842
r_scbond_it 2.686
r_mcangle_it 2.133
r_mcbond_it 1.501
r_nbd_refined 0.259
r_gen_planes_other 0.006
r_gen_planes_refined 0.009
r_chiral_restr 0.112
r_dihedral_angle_1_deg 6.328
r_angle_other_deg 1.019
r_angle_refined_deg 1.686
r_bond_other_d 0.008
r_bond_refined_d 0.016
r_nbd_other 0.262
r_nbtor_other 0.085
r_xyhbond_nbd_refined 0.124
r_metal_ion_refined 0.143
r_symmetry_vdw_refined 0.077
r_symmetry_vdw_other 0.33
r_symmetry_hbond_refined 0.147
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2804
Nucleic Acid Atoms 0
Heterogen Atoms 58
Solvent Atoms 521

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement
AMORE model building