Experiment: 3MD9

Structure of apo form of a periplasmic heme binding protein

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3MD8	PDB ENTRY 3MD8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	283	29% (w/v) PEG 5K MME, 0.1 M Magnesium acetate, 0.1 MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.71	α = 90
b = 66.74	β = 110.7
c = 62.27	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		PIXEL	PSI PILATUS 6M		2009-10-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.9191	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.48	29.13		0.089	0.089	14.24		78325	78325

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)
	1.48	1.52	97		0.528	4.31

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 3MD8	1.5	29.125	1.8	75064	5289	99.2	0.1541	0.1521	0.1516	0.1812	0.1798	Random

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]
0.757		0.567	-1.166		0.408

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.651
f_angle_d	1.195
f_chiral_restr	0.073
f_bond_d	0.009
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3730
Nucleic Acid Atoms
Solvent Atoms	537
Heterogen Atoms	18

Software

Software
Software Name	Purpose
XDS	data scaling
PHENIX	refinement
XDS	data reduction