2CFT

Crystal structure of human pyridoxal 5'-phosphate phosphatase with its substrate

X-RAY DIFFRACTION

---

Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.24	44.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.303	α = 90
b = 54.303	β = 90
c = 210.19	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC CCD		2005-07-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 4A		PAL/PLS	4A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.8	40	96	0.04	50	6.8		29341		2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.8	27.16	27818	1485	96.5	0.187	0.185	0.226	RANDOM	28.84

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.758
r_dihedral_angle_4_deg	15.369
r_dihedral_angle_3_deg	14.093
r_dihedral_angle_1_deg	5.763
r_scangle_it	4.16
r_scbond_it	2.627
r_mcangle_it	1.699
r_angle_refined_deg	1.526
r_mcbond_it	1.002
r_nbtor_refined	0.308
r_symmetry_vdw_refined	0.225
r_nbd_refined	0.208
r_xyhbond_nbd_refined	0.14
r_symmetry_hbond_refined	0.132
r_chiral_restr	0.105
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2187
Nucleic Acid Atoms
Solvent Atoms	235
Heterogen Atoms	18

Software

Software
Software Name	Purpose
REFMAC	refinement