Experiment: 3MGR

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1KX5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6	291	85mM MnCl2, 60mM KCl, 40mM K-cacodylate , pH 6.0, VAPOR DIFFUSION, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.462	α = 90
b = 109.681	β = 90
c = 182.213	γ = 90

Symmetry
Space Group	P 21 21 21

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 225 mm CCD	vertically collimating mirror	2009-06-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	0.81	SLS	X06DA

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	2.3	94.07	90.3	0.05	21.1	6.7	85891	84087			44.1

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	2.3	2.42	58.6		0.478	3.2	4.6	7966

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	1KX5	2.3	60	84087	1740	90.04	0.24242	0.24191	0.24	0.26735	0.26	RANDOM	60.23

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]
0.93			-3.12		2.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.11
r_dihedral_angle_4_deg	20.759
r_dihedral_angle_3_deg	15.624
r_dihedral_angle_1_deg	5.735
r_scangle_it	2.223
r_angle_refined_deg	1.472
r_mcangle_it	1.449
r_scbond_it	1.307
r_mcbond_it	0.839
r_nbtor_refined	0.303

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.11
r_dihedral_angle_4_deg	20.759
r_dihedral_angle_3_deg	15.624
r_dihedral_angle_1_deg	5.735
r_scangle_it	2.223
r_angle_refined_deg	1.472
r_mcangle_it	1.449
r_scbond_it	1.307
r_mcbond_it	0.839
r_nbtor_refined	0.303
r_symmetry_vdw_refined	0.204
r_nbd_refined	0.188
r_xyhbond_nbd_refined	0.139
r_symmetry_hbond_refined	0.092
r_chiral_restr	0.077
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6156
Nucleic Acid Atoms	6021
Solvent Atoms
Heterogen Atoms	23

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
REFMAC	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.