2A2N | pdb_00002a2n

Crystal Structure of the peptidylprolyl isomerase domain of Human PPWD1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1X07

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.7	298	1.7M NH4SO4, 0.1M sodium cacodylate pH 5.7, 0.2M sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.28	45.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 139.658	α = 90
b = 39.893	β = 122.33
c = 115.638	γ = 90

Symmetry
Space Group	C 1 2 1

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	mirrors	2005-04-07	M	SINGLE WAVELENGTH

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

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	1.65	23.2	91.4	0.036	34.86	3.4	59800	59800		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.71	63.1		2	2.6	4076

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	1X07	1.65	23.2	59800	56773	3027	91.43	0.20169	0.19939	0.21	0.24538	0.25	RANDOM	46.339

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]
-0.43		-1.5	1.67		-2.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.094
r_dihedral_angle_4_deg	17.979
r_dihedral_angle_3_deg	12.934
r_sphericity_free	7.413
r_sphericity_bonded	5.758
r_dihedral_angle_1_deg	5.73
r_scangle_it	4.955
r_scbond_it	3.743
r_mcangle_it	3.318
r_mcbond_it	2.54
r_rigid_bond_restr	2.25
r_angle_refined_deg	1.368
r_nbtor_refined	0.31
r_symmetry_vdw_refined	0.213
r_nbd_refined	0.208
r_symmetry_hbond_refined	0.201
r_xyhbond_nbd_refined	0.148
r_chiral_restr	0.098
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3865
Nucleic Acid Atoms
Solvent Atoms	388
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing