2Z3W | pdb_00002z3w

Prolyl tripeptidyl aminopeptidase mutant E636A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2D5L	PDB ENTRY 2D5L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	293	1.1M potassium sodium tartrate, 0.2M lithium sulfate, 0.1M CHES buffer, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.27	62.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 149.709	α = 90
b = 149.709	β = 90
c = 160.943	γ = 120

Symmetry
Space Group	P 63 2 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	monochrometor	2006-11-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.000	Photon Factory	BL-5A

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	2	50	99.9	0.064	81	20	71953	71953			31.5

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	2	2.07	99.6		0.314	11.6	19.1	7036

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 2D5L	2	20	66242	66242	3533	97.01	0.18753	0.186	0.19	0.21609	0.22	RANDOM	36.773

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]
-0.59	-0.29		-0.59		0.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.639
r_dihedral_angle_4_deg	16.622
r_dihedral_angle_3_deg	14.575
r_dihedral_angle_1_deg	6.442
r_scangle_it	3.628
r_scbond_it	2.402
r_mcangle_it	1.561
r_angle_refined_deg	1.449
r_mcbond_it	0.989
r_nbtor_refined	0.31
r_nbd_refined	0.199
r_symmetry_hbond_refined	0.159
r_symmetry_vdw_refined	0.156
r_xyhbond_nbd_refined	0.14
r_chiral_restr	0.109
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5193
Nucleic Acid Atoms
Solvent Atoms	547
Heterogen Atoms	11

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling