4PWY

Crystal structure of a Calmodulin-lysine N-methyltransferase fragment

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4LEC	FFAS03/SCWRL-modified models of PDB entries 4lec, 3bzb, 4lg1, 4mtl
experimental model	PDB	3BZB	FFAS03/SCWRL-modified models of PDB entries 4lec, 3bzb, 4lg1, 4mtl
experimental model	PDB	4LG1	FFAS03/SCWRL-modified models of PDB entries 4lec, 3bzb, 4lg1, 4mtl
experimental model	PDB	4MTL	FFAS03/SCWRL-modified models of PDB entries 4lec, 3bzb, 4lg1, 4mtl

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.7	291	2.0 M malonate, pH 6.7, vapor diffusion, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.5	64.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.935	α = 90
b = 80.935	β = 90
c = 121.952	γ = 90

Symmetry
Space Group	P 41 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		2014-01-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E	1.5418

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	1.9	50	100	0.107	9	13.9		32722

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	1.9	1.93	100		0.939		13.7	1611

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	FFAS03/SCWRL-modified models of PDB entries 4lec, 3bzb, 4lg1, 4mtl	1.9	25	32627	1573	99.9	0.1614	0.1599	0.1914	RANDOM	22.9872

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]
-0.05			-0.05		0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.521
r_dihedral_angle_4_deg	19.027
r_dihedral_angle_3_deg	13.412
r_dihedral_angle_1_deg	6.066
r_mcangle_it	3.645
r_mcbond_other	2.556
r_mcbond_it	2.555
r_angle_refined_deg	1.518
r_angle_other_deg	0.822
r_chiral_restr	0.093
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1979
Nucleic Acid Atoms
Solvent Atoms	106
Heterogen Atoms	64

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction