2QDJ

Crystal structure of the Retinoblastoma protein N-domain provides insight into tumor suppression, ligand interaction and holoprotein architecture

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	277	0.2 M Na acetate, 25% (w/v) PEG 4000, 0.1 M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.296	α = 90
b = 106.649	β = 90
c = 98.191	γ = 90

Symmetry
Space Group	C 2 2 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	CCD	ADSC QUANTUM 4		2005-10-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.93300	ESRF	ID14-2

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	2	51.1	99.5	0.059	14.7	4		25840

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)
	2	2.11	99.4		0.304	3.9	4.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2	51.1	24550	1288	99.22	0.23064	0.22834	0.27609	RANDOM	34.938

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]
-0.5			-0.95		1.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.512
r_dihedral_angle_4_deg	23.965
r_dihedral_angle_3_deg	16.89
r_scangle_it	5.03
r_dihedral_angle_1_deg	4.792
r_scbond_it	3.866
r_mcangle_it	3.421
r_mcbond_it	2.479
r_angle_refined_deg	1.189
r_nbtor_refined	0.326
r_symmetry_vdw_refined	0.288
r_nbd_refined	0.242
r_symmetry_hbond_refined	0.127
r_xyhbond_nbd_refined	0.118
r_chiral_restr	0.102
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2117
Nucleic Acid Atoms
Solvent Atoms	234
Heterogen Atoms

Software

Software
Software Name	Purpose
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction
SCALA	data scaling