2VFX | pdb_00002vfx

Structure of the Symmetric Mad2 Dimer

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	VAPOR DIFFUSION, HANGING DROP, 20 DEGREES C. 1 MICROLITER PROTEIN: 3 MG/ML IN 20 MM TRIS, PH 8.0, 50 MM NACL, 2 MM TCEP PLUS 1 MICROLITER RESERVOIR: 19% PEG2000, 16% GLYCEROL, 100 MM TRIS, PH 8.0, 0.3 M MGCL2

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.337	α = 90
b = 191.407	β = 90.02
c = 154.307	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	CCD	ADSC CCD		2006-08-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID		APS	19-ID

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	1.95	45.37	97.7	0.07	14.9	2.9		223558		-3	23.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	1.98	95.7		0.55	1.6	2.6

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 1KLQ	1.95	45	220725	2700	97.3	0.209	0.208	0.21	0.247	0.24	RANDOM	25.39

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]
0.81		0.2	-0.83		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.022
r_dihedral_angle_4_deg	18.857
r_dihedral_angle_3_deg	14.773
r_scangle_it	2.877
r_dihedral_angle_1_deg	2.008
r_scbond_it	1.788
r_angle_refined_deg	1.501
r_mcangle_it	1.156
r_mcbond_it	0.706
r_nbtor_refined	0.306
r_symmetry_hbond_refined	0.211
r_nbd_refined	0.199
r_symmetry_vdw_refined	0.171
r_xyhbond_nbd_refined	0.139
r_chiral_restr	0.096
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19613
Nucleic Acid Atoms
Solvent Atoms	1591
Heterogen Atoms	151

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing