Crystal Structures of Human Prostatic Acid Phosphatase in Complex with a Phosphate Ion and alpha-Benzylaminobenzylphosphonic Acid Update the Mechanistic Picture and Offer New Insights into Inhibitor Design

X-RAY DIFFRACTION Experimental Data & Validation

X-ray Experimental Help


Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 10
Temperature 298.0
Details PEG, KCL, Glycine, pH 10.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 120.1 α = 90
b = 204.86 β = 90
c = 71.22 γ = 90
Space Group P 21 21 21


Diffraction Experiment
ID # Data Collection Temperature
1 298
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV Yale Mirrors 1997-12-01
Diffraction Radiation
Monochromator Protocol
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline

Data Collection

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
2.89 50 82.2 0.063 -- -- -- 33191 33191 -- -- 74.4
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)
2.89 3.0 63.7 -- -- -- -- --


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
FOURIER SYNTHESIS 2.9 77.94 -- 0.0 33191 31444 1557 78.9 -- 0.2051 0.205 0.279 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 2.9 3.08 -- 219 3773 0.269 0.367 0.025 60.9
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 30.0
Anisotropic B[1][1] -1.95
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.52
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 4.47
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 0.87
c_dihedral_angle_d 22.4
c_angle_deg 1.4
c_bond_d 0.01
Coordinate Error
Parameter Value
Luzzati ESD (R-Free Set) 0.46
Luzzati Sigma A (R-Free Set) 0.5
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 11196
Nucleic Acid Atoms 0
Heterogen Atoms 396
Solvent Atoms 135


Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
CNS 1.1 Structure Refinement
Software Name Purpose
CNS version: 1.1 refinement
CNS model building
SCALEPACK data reduction
HKL-2000 data collection