2OKN | pdb_00002okn

Crystal Strcture of Human Prolidase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2IW2	PDB ENTRY 2iw2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	298	1.5M sodium/potassium phosphate, 0.05M sodium chloride, 0.02% sodium acide, 0.02M dithiothreitol, 0.02M manganese chloride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.89	α = 90
b = 108.96	β = 90
c = 212.01	γ = 90

Symmetry
Space Group	C 2 2 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	CCD	MAR CCD 165 mm		2004-02-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1		BESSY	14.1

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	2.45	37.53	99.7	0.041	0.041	26.2	4.14	44429	44429			31.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.45	2.5	100		0.14	0.14	9.7	4.16	2626

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 2iw2	2.45	36.94	44426	44426	2221	100	0.18	0.18	0.178	0.1802	0.231	0.2304	RANDOM	41.144

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]
0.91			-2.42		1.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.431
r_dihedral_angle_4_deg	18.634
r_dihedral_angle_3_deg	16.054
r_dihedral_angle_1_deg	6.136
r_mcangle_it	1.635
r_scangle_it	1.564
r_angle_refined_deg	1.393
r_scbond_it	1.058
r_mcbond_it	1.036
r_symmetry_vdw_refined	0.321
r_nbtor_refined	0.303
r_symmetry_hbond_refined	0.267
r_nbd_refined	0.205
r_xyhbond_nbd_refined	0.133
r_chiral_restr	0.095
r_bond_refined_d	0.013
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7432
Nucleic Acid Atoms
Solvent Atoms	301
Heterogen Atoms	19

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
XSCALE	data scaling