4QPN | pdb_00004qpn

Crystal Structure of Human Methyltransferase-Like Protein 21B

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4LEC	solved with data from isomorphous crystal. model based on pdb entry 4LEC.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	20% PEG-3350, 0.2 M tri-lithium citrate. Protein sample was incubated with SAH overnight. Endopeptidase was added to the protein sample immediately prior to crystallization set up, vapor diffusion, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.67	26.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.665	α = 90
b = 38.665	β = 90
c = 193.915	γ = 120

Symmetry
Space Group	P 61

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 q315		2014-06-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97915	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	1.25	38.78	100	0.092	19.6	11.1		45170

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	1.25	1.27	100		0.956	3	10.8	2181

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	solved with data from isomorphous crystal. model based on pdb entry 4LEC.	1.25	33.48	45060	2190	99.95	0.1238	0.1216	0.136	0.1667	0.1756	RANDOM	12.1595

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	0.01		0.03		-0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.43
r_sphericity_free	19.118
r_dihedral_angle_4_deg	18.485
r_dihedral_angle_3_deg	12.301
r_sphericity_bonded	8.001
r_dihedral_angle_1_deg	6.948
r_rigid_bond_restr	4.623
r_mcangle_it	1.99
r_angle_refined_deg	1.98
r_mcbond_other	1.568
r_mcbond_it	1.567
r_angle_other_deg	0.899
r_chiral_restr	0.128
r_bond_refined_d	0.019
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1579
Nucleic Acid Atoms
Solvent Atoms	202
Heterogen Atoms	50

Software

Software
Software Name	Purpose
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction