Experiment: 3GWZ

Structure of the Mitomycin 7-O-methyltransferase MmcR

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	Protein solution (10 mg/ml MmcR Protein, 0.05 M NaCl, 0.02 M Tris pH 8) mixed in a 1:1 ratio with the well solution (10% PEG4K, 15% MPD, 0.1 M CaCl2, 0.1 M MES pH 6.0) Cryoprotected with 25% ethylene glycol, 10% PEG4K, 15% MPD, 0.1 M CaCl2, 0.1 M MES pH 6.0, vapor diffusion, hanging drop, temperature 277K, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.372	α = 90
b = 98.918	β = 90
c = 171.119	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 300 mm CCD	Adjustable focusing mirrors in K-B geometry	2008-07-31	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97945,0.96421	APS	23-ID-D

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	1.91	50	98.6	0.113	11.545	13.6		115235

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	1.91	1.98	87.9		0.57	2.428	9.2	10169

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MAD	1.91	19.653	1.32	114971	5763	98.94	0.176	0.174	0.21	0.2074	23.386

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]
0.051			0.037		-0.081

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.181
f_angle_d	1
f_chiral_restr	0.064
f_bond_d	0.006
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10296
Nucleic Acid Atoms
Solvent Atoms	871
Heterogen Atoms	140

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
DM	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling