X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 277.15
Details We soaked monoclinic crystals of HCAII with BTA (EVF) by carrying out the following steps: (i) We prepared soaking solutions containing 1.32 M sodium citrate, 1 mM ZnSO4, 100 mM Tris-HCl (pH 7.8), and 5 mM ligand. (ii) We combined 4 uL of soaking solution and 1-2 crystals of HCAII within a drop on the surface of a reservoir cover (EasyXtal CrystalSupport, Qiagen). (iii) To a clear plastic reservoir in a 15-reservoir plate (EasyXtal, Qiagen), we added 1 mL of soaking solution (without ligand present). We attached the reservoir cover to the reservoir and left the entire setup at 4 deg C for 1 week.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.35 α = 90
b = 41.88 β = 104.63
c = 72.06 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 QUANTUM 315r -- 2015-04-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.2.1 1.1 ALS 8.2.1

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
1.11 40.02 74.65 -- -- -- 3.7 -- 141290 -- -- --
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)
-- -- -- -- -- -- -- --

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 1.11 40.018 -- 1.35 -- 141290 3666 74.65 -- 0.1193 0.1189 0.1314 --
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 1.1102 1.1249 -- 8 250 0.2564 0.281 -- 4.0
X Ray Diffraction 1.1249 1.1403 -- 8 645 0.2454 0.2137 -- 9.0
X Ray Diffraction 1.1403 1.1566 -- 18 1059 0.226 0.2279 -- 15.0
X Ray Diffraction 1.1566 1.1738 -- 50 1563 0.1877 0.2534 -- 22.0
X Ray Diffraction 1.1738 1.1922 -- 73 2171 0.1525 0.1839 -- 31.0
X Ray Diffraction 1.1922 1.2117 -- 69 2798 0.137 0.2372 -- 40.0
X Ray Diffraction 1.2117 1.2326 -- 84 3549 0.1214 0.1339 -- 50.0
X Ray Diffraction 1.2326 1.255 -- 123 4152 0.117 0.1434 -- 59.0
X Ray Diffraction 1.255 1.2792 -- 137 4904 0.1153 0.1444 -- 69.0
X Ray Diffraction 1.2792 1.3053 -- 123 5623 0.1083 0.1542 -- 79.0
X Ray Diffraction 1.3053 1.3337 -- 204 6299 0.1096 0.1346 -- 90.0
X Ray Diffraction 1.3337 1.3647 -- 164 6693 0.1082 0.1098 -- 93.0
X Ray Diffraction 1.3647 1.3988 -- 179 6712 0.1091 0.1215 -- 95.0
X Ray Diffraction 1.3988 1.4366 -- 190 6876 0.1094 0.1281 -- 97.0
X Ray Diffraction 1.4366 1.4789 -- 182 6965 0.1094 0.1463 -- 98.0
X Ray Diffraction 1.4789 1.5266 -- 189 6978 0.1081 0.1266 -- 98.0
X Ray Diffraction 1.5266 1.5812 -- 167 6976 0.1039 0.1336 -- 99.0
X Ray Diffraction 1.5812 1.6445 -- 189 7033 0.1077 0.1448 -- 99.0
X Ray Diffraction 1.6445 1.7194 -- 189 7018 0.1116 0.1228 -- 99.0
X Ray Diffraction 1.7194 1.81 -- 187 7083 0.1128 0.1423 -- 99.0
X Ray Diffraction 1.81 1.9234 -- 184 7053 0.1108 0.1225 -- 99.0
X Ray Diffraction 1.9234 2.0719 -- 177 6986 0.113 0.1127 -- 99.0
X Ray Diffraction 2.0719 2.2804 -- 206 7048 0.1135 0.121 -- 100.0
X Ray Diffraction 2.2804 2.6103 -- 188 7086 0.125 0.1477 -- 100.0
X Ray Diffraction 2.6103 3.2885 -- 189 7057 0.1313 0.1372 -- 99.0
X Ray Diffraction 3.2885 40.0436 -- 189 7047 0.1303 0.1176 -- 99.0
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.011
f_chiral_restr 0.083
f_dihedral_angle_d 13.012
f_plane_restr 0.008
f_angle_d 1.364
Coordinate Error
Parameter Value
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2072
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 444

Software

Software
Software Name Purpose
PHENIX refinement version: dev_1839
xia2 data reduction
PHASER phasing
xia2 data scaling