2HE9 | pdb_00002he9

Structure of the peptidylprolyl isomerase domain of the human NK-tumour recognition protein

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ZCX	pdb entry 1ZCX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	Well solution: 21% Peg 3350, 0.25M potassium sulfate; Protein solution: 50 mM Tris pH 7.5, 100 mM NaCl, 1 mM DTT, 15 mg/mL protein, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.753	α = 90
b = 72.786	β = 90
c = 73.014	γ = 90

Symmetry
Space Group	P 21 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	IMAGE PLATE	RIGAKU RAXIS IV		2006-06-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	20	99.9	0.146	15.2	7	23807	23807		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2	2.07	98.7		0.769		6.5	2317

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	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1ZCX	2	19.91	23772	22557	1215	99.9	0.14889	0.14631	0.15	0.19752	0.2	RANDOM	20.605

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]
-0.82			1.59		-0.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.13
r_dihedral_angle_4_deg	20.046
r_dihedral_angle_3_deg	12.663
r_dihedral_angle_1_deg	6.306
r_scangle_it	5.543
r_scbond_it	4.025
r_mcangle_it	2.503
r_mcbond_it	2.12
r_angle_refined_deg	1.515
r_nbtor_refined	0.315
r_nbd_refined	0.203
r_symmetry_vdw_refined	0.175
r_symmetry_hbond_refined	0.128
r_xyhbond_nbd_refined	0.122
r_chiral_restr	0.111
r_bond_refined_d	0.017
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2708
Nucleic Acid Atoms
Solvent Atoms	275
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
PHASER	phasing