2RJD | pdb_00002rjd

Crystal structure of L3MBTL1 protein

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PQW	PDB entry 2PQW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	300	4% PEG 4000, 0.1M Sodium acetate, 1mM H1bK26me2 peptide, 0.1 M Sodium acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K

Crystal Properties
Matthews coefficient	Solvent content
3.15	60.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.518	α = 90
b = 94.195	β = 90
c = 59.009	γ = 90

Symmetry
Space Group	P 21 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	varimax	2006-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ DW	1.54000

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	1.65	34.63	98.5	0.057		5.7	57382	57382

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 2PQW	1.65	34.63	54435	54435	2901	98.3	0.20374	0.20374	0.20233	0.2	0.23008	0.23	RANDOM	29.596

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]
-0.21			0.15		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.587
r_dihedral_angle_4_deg	21.092
r_dihedral_angle_3_deg	13.996
r_dihedral_angle_1_deg	6.138
r_scangle_it	3.229
r_scbond_it	2.177
r_mcangle_it	1.626
r_angle_refined_deg	1.342
r_mcbond_it	0.928
r_nbtor_refined	0.307
r_nbd_refined	0.205
r_symmetry_vdw_refined	0.185
r_symmetry_hbond_refined	0.174
r_xyhbond_nbd_refined	0.133
r_chiral_restr	0.102
r_bond_refined_d	0.012
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	2608
Nucleic Acid Atoms
Solvent Atoms	521
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing