X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.5
Details ACTIVE F1-ATPASE (12 MG/ML) WAS EXCHANGED ON A DESALTING COLUMN INTO CRYSTALLISATION BUFFER, PREPARED IN D2O CONSISTING OF 100 MM BIS-TRIS PROPANE, PH 7.5, 100 MM SUCROSE, 1 MM ADP AND 10 MM MAGNESIUM SULPHATE. THEN THE ENZYME WAS INHIBITED AT 23C WITH A 4-FOLD MOLAR EXCESS OF YI1-53 (MUTATION E21A) IN THE PRESENCE OF 1 MM ATP AND 2 MM MAGNESIUM SULPHATE. FURTHER PORTIONS (5 UL OF A NEUTRALISED STOCK SOLUTION CONTAINING 200 MM ATP AND 400 MM MAGNESIUM SULPHATE/ML PROTEIN SOLUTION) WERE ADDED AFTER 5 AND 10 MIN. MORE THAN 95% OF THE ATP HYDROLYSIS ACTIVITY OF THE ENZYME WAS INHIBITED. SODIUM-POTASSIUM TARTRATE WAS ADDED TO 100 MM, AND THE CONCENTRATION OF THE PROTEIN SOLUTION WAS ADJUSTED TO 10 MG/ML WITH CRYSTALLISATION BUFFER. CRYSTALS WERE GROWN AT 23C IN 72 WELL MICRO-BATCH PLATES UNDER FILTERED PARAFFIN OIL. THE CRYSTALLISATION DROPS (4 UL) CONTAINED A 1:1 MIXTURE OF PROTEIN SOLUTION AND PRECIPITANT SOLUTION (20%-26% POLYETHYLENE GLYCOL 3000 AND 600 MM NACL PREPARED IN D2O).

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 118.22 α = 90
b = 187.85 β = 89.96
c = 181.81 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 MARRESEARCH -- 2009-10-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I24 -- DIAMOND I24

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
2.5 43.84 98.4 0.11 -- -- 3.9 -- 268620 -- 3.0 --
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)
2.5 2.64 97.6 0.75 -- 2.0 3.9 --

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 2.5 181.81 -- -- -- 254974 13570 98.25 -- 0.22618 0.2243 0.26194 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 2.5 2.565 -- 996 18559 0.335 0.36 -- 96.87
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 60.332
Anisotropic B[1][1] 0.18
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.46
Anisotropic B[2][2] 0.66
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.84
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.592
r_scbond_it 2.688
r_mcangle_it 1.084
r_mcbond_it 0.576
r_gen_planes_refined 0.004
r_chiral_restr 0.075
r_dihedral_angle_4_deg 16.409
r_dihedral_angle_3_deg 16.365
r_dihedral_angle_2_deg 35.082
r_dihedral_angle_1_deg 5.472
r_angle_refined_deg 1.175
r_bond_refined_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 50724
Nucleic Acid Atoms 0
Heterogen Atoms 366
Solvent Atoms 773

Software

Computing
Computing Package Purpose
IMOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.5.0110 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0110 refinement
PHASER model building