1O9K

Crystal structure of the retinoblastoma tumour suppressor protein bound to E2F peptide

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.8		pH 7.80

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.996	α = 90
b = 158.548	β = 93.7
c = 110.617	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	85					M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID13		ESRF	ID13

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	2.6	50	88.1	0.094	9.1	8.8		53846

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	2.6	2.69

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1GUX	2.6	20	44963	2386	88.2	0.232	0.229	0.23	0.285	RANDOM	38.28

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]
-1.51		0.47	-0.56		2.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	19.414
r_dihedral_angle_1_deg	2.502
r_scangle_it	1.888
r_angle_refined_deg	1.368
r_mcangle_it	1.341
r_scbond_it	1.129
r_mcbond_it	0.71
r_symmetry_hbond_refined	0.659
r_symmetry_vdw_refined	0.332
r_nbd_refined	0.29
r_xyhbond_nbd_refined	0.246
r_chiral_restr	0.087
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
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	11724
Nucleic Acid Atoms
Solvent Atoms	250
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing