X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 293.0
Details A THREE-FOLD EXCESS OF A PROPRIETARY FACTOR XA INHIBITOR WITH PICOMOLAR AFFINITY WAS ADDED TO THE DES-GLA-FACTOR XA. THIS INHIBITOR IS BASED ON THE SAME TEMPLATE AS XLC IN 1MQ5. THE PROTEIN WAS THEN CONCENTRATED TO 12-17 MG/ML. CRYSTALS WERE GROWN USING 2 UL OF COMPLEX WITH 2 UL OF RESERVOIR CONTAINING 15-21% PEG1500 AND 10 MM CACL2. 30-40 UL SITTING DROPS CONTAINING SATURATED INHIBITOR (5 MM) IN 21% PEG1500, 5 MM CACL2, 50 MM NACL, 50 MM TRIS PH 7.5 (CRYSTAL SOAKING SOLUTION) WERE EQUILIBRATED OVER A 1 ML RESERVOIR CONTAINING THE CRYSTAL SOAKING SOLUTION FOR 1 TO 2 DAYS. A SINGLE FACTOR XA CRYSTAL WAS TRANSFERRED USING A MOUNTED CRYOLOOP INTO ONE OF THESE SITTING DROPS AND ALLOWED TO SOAK FOR THREE OR MORE Days. AFTER THE INITIAL SOAK, EACH CRYSTAL WAS THEN TRANSFERRED TO AN UNUSED DROP AND ALLOWED TO SOAK FOR SECOND PERIOD OF THREE OR MORE DAYS. pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 56.36 α = 90
b = 72.02 β = 90
c = 78.92 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 2000-12-06
Diffraction Radiation
Monochromator Protocol
SI(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL7-1 1.08 SSRL BL7-1

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
2.1 25 98.4 -- 0.054 -- 3.6 18977 18977 0.0 0.0 30.79
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)
2.1 2.15 97.3 -- 0.395 2.2 3.7 1366

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
DIRECT REPLACEMENT 2.1 8.0 0.0 2.0 18977 18602 720 98.2 -- 0.1926 0.19 0.264 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 2.1 2.19 2120 91 2120 0.284 0.3439 -- --
X Ray Diffraction 2.19 2.31 2137 80 -- 0.2719 0.2936 -- --
X Ray Diffraction 2.31 2.45 2129 88 -- 0.2358 0.299 -- --
X Ray Diffraction 2.45 2.63 2181 91 -- 0.2311 0.277 -- --
X Ray Diffraction 2.63 2.88 2200 84 -- 0.2101 0.2684 -- --
X Ray Diffraction 2.88 3.28 2216 110 -- 0.1887 0.2798 -- --
X Ray Diffraction 3.28 4.04 2137 82 -- 0.1491 0.2447 -- --
X Ray Diffraction 4.04 8.0 2343 94 -- 0.1561 0.2343 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 31.18
Anisotropic B[1][1] -3.5382
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 4.9249
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.3866
RMS Deviations
Key Refinement Restraint Deviation
x_improper_angle_d 1.56
x_bond_d 0.011
x_angle_deg 2.02
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2220
Nucleic Acid Atoms 0
Heterogen Atoms 53
Solvent Atoms 172

Software

Computing
Computing Package Purpose
MAR Data Reduction (intensity integration)
MOSFLM Data Reduction (data scaling)
X-PLOR 3.1 Structure Solution
X-PLOR 3.1 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.1 refinement
X-PLOR version: 3.1 model building
MOSFLM data reduction
MAR data collection