Experiment: 2X9I

Structure of the Mutant D105N of Phycoerythrobilin Synthase PebS from the Cyanophage P-SSM2 in complex with bound substrate Biliverdin IXA

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VGR	PDB ENTRY 2VGR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				170MM (NH4)2SO4, 20%PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.58	52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.92	α = 109.38
b = 70.14	β = 109.25
c = 81.97	γ = 92.56

Symmetry
Space Group	P 1

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	DECTRIS PILATUS 6M	MIRRORS	2008-12-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA		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	2.2	43	96.6	0.07	10.56	2.7		50826			29.43

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	2.2	2.26	96.6		0.29	3.73	2.8

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 2VGR	2.2	43.01	2	50817	2561	96.84	0.1783	0.1764	0.1733	0.2115	0.2071

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]
-6.5789	-0.8586	0.9726	14.1141	7.3864	-7.5353

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	18.106
f_angle_d	1.435
f_chiral_restr	0.096
f_bond_d	0.012
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6870
Nucleic Acid Atoms
Solvent Atoms	349
Heterogen Atoms	182

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing