2NSZ | pdb_00002nsz

1.15 Angstrom Crystal Structure of the MA3 domain of Pdcd4

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	293	0.17 M ammonium sulfate, 0.085 M sodium acetate, 25.5% (w/v) PEG 2000 MME, 15% (v/v) glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.83	56.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.52	α = 90
b = 61.52	β = 90
c = 77.751	γ = 120

Symmetry
Space Group	P 31 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	CCD	MAR CCD 165 mm		2006-06-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.00000	APS	22-ID

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	1.15	28.6	97	0.06	28.2	7.1	61054	59292		1	17.4

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	1.15	1.18	99.91		0.465	4.54	7	4263

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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 2ION	1.15	28.6	57917	3093	99.94	0.13316	0.13228	0.13	0.14959	0.15	RANDOM	10.826

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]
0.19	0.1		0.19		-0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.557
r_dihedral_angle_4_deg	16.331
r_dihedral_angle_3_deg	10.902
r_sphericity_free	6.354
r_dihedral_angle_1_deg	4.14
r_scangle_it	4.036
r_sphericity_bonded	3.496
r_scbond_it	2.974
r_mcangle_it	2.104
r_mcbond_it	1.717
r_rigid_bond_restr	1.491
r_angle_refined_deg	1.451
r_angle_other_deg	0.864
r_mcbond_other	0.598
r_symmetry_hbond_refined	0.358
r_symmetry_vdw_other	0.25
r_nbd_refined	0.241
r_symmetry_vdw_refined	0.228
r_nbtor_refined	0.186
r_nbd_other	0.164
r_xyhbond_nbd_refined	0.152
r_chiral_restr	0.096
r_nbtor_other	0.085
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1037
Nucleic Acid Atoms
Solvent Atoms	170
Heterogen Atoms	16

Software

Software
Software Name	Purpose
REFMAC	refinement