2P27 | pdb_00002p27

Crystal Structure of Human Pyridoxal Phosphate Phosphatase with Mg2+ at 1.9 A resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2YOC	PDB entry 2YOC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	298	100mM Tris-HCl pH 8.5, 17% PEG 20000, 100mM Magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.245	α = 90
b = 54.245	β = 90
c = 213.182	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 QUANTUM 315		2007-02-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.97900	NSLS	X29A

Data Collection

Overall
ID #	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	1.9	50	100	0.068	0.052	9.5	8.3	26274	26274

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.9	1.97	100		0.624		8.2	4819

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2YOC	1.9	48.34	26182	26182	1332	99.98	0.213	0.213	0.211	0.21	0.25	0.25	RANDOM	32.203

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]
0.29			0.29		-0.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.997
r_dihedral_angle_4_deg	17.508
r_dihedral_angle_3_deg	15.049
r_dihedral_angle_1_deg	7.347
r_scangle_it	3.453
r_scbond_it	2.199
r_mcangle_it	1.538
r_angle_refined_deg	1.454
r_mcbond_it	0.906
r_nbtor_refined	0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.997
r_dihedral_angle_4_deg	17.508
r_dihedral_angle_3_deg	15.049
r_dihedral_angle_1_deg	7.347
r_scangle_it	3.453
r_scbond_it	2.199
r_mcangle_it	1.538
r_angle_refined_deg	1.454
r_mcbond_it	0.906
r_nbtor_refined	0.3
r_nbd_refined	0.203
r_xyhbond_nbd_refined	0.16
r_symmetry_hbond_refined	0.143
r_symmetry_vdw_refined	0.13
r_chiral_restr	0.088
r_metal_ion_refined	0.022
r_bond_refined_d	0.011
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2236
Nucleic Acid Atoms
Solvent Atoms	116
Heterogen Atoms	1

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.