3CKK | pdb_00003ckk

Crystal structure of human methyltransferase-like protein 1

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	297	2.0 M Ammonium sulfate, 2% PEG 400, 0.1 M Na HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.316	α = 90
b = 90.316	β = 90
c = 54.94	γ = 120

Symmetry
Space Group	P 65

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	MARMOSAIC 300 mm CCD	Si(111)	2008-03-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.03310	APS	23-ID-B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.55	100	99.1	0.068	0.068	13.2	11.2	36869	36869			23.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.61	91.3		0.596	0.596	1.78	4.5	3389

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 2VDU	1.55	50	36089	36089	750	99.04	0.19962	0.19962	0.19922	0.2	0.21835	0.22	RANDOM	24.817

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]
-0.03	-0.02		-0.03		0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.964
r_dihedral_angle_4_deg	15.429
r_dihedral_angle_3_deg	12.368
r_dihedral_angle_1_deg	5.067
r_scangle_it	2.708
r_scbond_it	1.944
r_mcangle_it	1.4
r_angle_refined_deg	1.276
r_mcbond_it	0.798
r_nbtor_refined	0.309
r_nbd_refined	0.193
r_symmetry_vdw_refined	0.152
r_xyhbond_nbd_refined	0.125
r_symmetry_hbond_refined	0.116
r_chiral_restr	0.084
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
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	1533
Nucleic Acid Atoms
Solvent Atoms	235
Heterogen Atoms	33

Software

Software
Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
ARP/wARP	model building
Coot	model building