Experiment: 3MGP

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
2.72	54.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.502	α = 90
b = 109.94	β = 90
c = 183.352	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	PIXEL	PSI PILATUS 6M	Dynamically bendable mirror	2009-06-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.6	SLS	X06SA

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	2.44	94.49	91.6	0.063	17	4.7	73764	72231			64

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	2.44	2.57	59.5		0.442	1	2.1	6843

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	2.44	52.6	72231	1466	91.3	0.24022	0.23935	0.242	0.28245	0.2799	RANDOM	83.713

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]
1.44			-3.08		1.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.484
r_dihedral_angle_4_deg	20.863
r_dihedral_angle_3_deg	17.763
r_dihedral_angle_1_deg	5.909
r_scangle_it	2.127
r_angle_refined_deg	1.433
r_mcangle_it	1.375
r_scbond_it	1.195
r_mcbond_it	0.777
r_nbtor_refined	0.302

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.484
r_dihedral_angle_4_deg	20.863
r_dihedral_angle_3_deg	17.763
r_dihedral_angle_1_deg	5.909
r_scangle_it	2.127
r_angle_refined_deg	1.433
r_mcangle_it	1.375
r_scbond_it	1.195
r_mcbond_it	0.777
r_nbtor_refined	0.302
r_nbd_refined	0.195
r_symmetry_vdw_refined	0.184
r_xyhbond_nbd_refined	0.145
r_symmetry_hbond_refined	0.099
r_chiral_restr	0.074
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6160
Nucleic Acid Atoms	6021
Solvent Atoms
Heterogen Atoms	47

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.