3EDY | pdb_00003edy

Crystal Structure of the Precursor Form of Human Tripeptidyl-Peptidase 1

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	278	PEG 6000, citrate, pH 5.0, vapor diffusion, hanging drop, temperature 278K

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.807	α = 90
b = 93.173	β = 90
c = 102.479	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate	mirrors	2007-10-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4C	0.97908	NSLS	X4C

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	1.83	50	99.1	0.079		7	48561	50890			37

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	1.83	1.9	93.1		0.457	2.3	4.8	4675

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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		THROUGHOUT	1.85	29.72	48561	48127	1231	97.01	0.179	0.179	0.1975	0.205	0.2155	RANDOM	26.882

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]
-0.03			0.13		-0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.405
r_dihedral_angle_4_deg	15.069
r_dihedral_angle_3_deg	13.894
r_dihedral_angle_1_deg	7.328
r_scangle_it	4.871
r_scbond_it	3.351
r_mcangle_it	2.165
r_mcbond_it	1.466
r_angle_refined_deg	1.263
r_angle_other_deg	1.038
r_mcbond_other	0.462
r_symmetry_vdw_other	0.291
r_nbd_other	0.227
r_nbd_refined	0.226
r_nbtor_refined	0.191
r_symmetry_vdw_refined	0.188
r_xyhbond_nbd_refined	0.146
r_metal_ion_refined	0.135
r_symmetry_hbond_refined	0.109
r_nbtor_other	0.106
r_chiral_restr	0.088
r_gen_planes_refined	0.012
r_bond_refined_d	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4195
Nucleic Acid Atoms
Solvent Atoms	235
Heterogen Atoms	73

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
SOLVE	phasing