3EBQ | pdb_00003ebq

Crystal structure of human PPPDE1

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	293	10% PEG 4000, 0.1 M SODIUM, ACETATE, 0.1 M TRIS HCL PH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K. CRYSTALS WERE SOAKED OVERNIGHT IN 0.01 M THIMEROSAL TO CREATE THE MERCURY DERIVATIVE.

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.625	α = 90
b = 41.625	β = 90
c = 184.239	γ = 90

Symmetry
Space Group	P 43 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		2008-08-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.54178

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	1.9	30	98.4	0.068	45.21	11.4	13493	13493		-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)
	1.9	1.97	87.9		0.646	2.57	5.7	1162

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	SAD	THROUGHOUT	1.9	28.04	13493	12727	670	98.19	0.22585	0.22354	0.2213	0.27273	0.2651	RANDOM	38.566

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]
0.32			0.32		-0.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.969
r_dihedral_angle_4_deg	21.889
r_dihedral_angle_3_deg	12.825
r_dihedral_angle_1_deg	6.323
r_scangle_it	3.524
r_scbond_it	2.439
r_angle_refined_deg	1.63
r_mcangle_it	1.505
r_mcbond_it	1.012
r_nbtor_refined	0.309
r_nbd_refined	0.218
r_symmetry_vdw_refined	0.205
r_xyhbond_nbd_refined	0.151
r_symmetry_hbond_refined	0.147
r_chiral_restr	0.103
r_bond_refined_d	0.017
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1124
Nucleic Acid Atoms
Solvent Atoms	63
Heterogen Atoms	3

Software

Software
Software Name	Purpose
SBC-Collect	data collection
SOLVE	phasing
RESOLVE	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
RESOLVE	phasing