Experiment: 2ZZL

Structure of bacteriorhodopsin's M intermediate at pH 7

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1IW9	PDB ENTRY 1iw9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Membrane fusion method	5.2	293	2.2M ammonium sulfate, 0.1M sodium citrate, 0.16M potasium chloride, 3M ammonium sulfate, 0.1M HEPES pH 7, liquid propane, Membrane fusion method, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3	59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.21	α = 90
b = 102.21	β = 90
c = 112.48	γ = 120

Symmetry
Space Group	P 6 2 2

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	MAR CCD 165 mm		2009-01-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	0.912	Photon Factory	AR-NW12A

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	2.03	44.2	93.7	0.084	0.084	22.8	14.4	23074	21621			31.68

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.03	2.43	71.4		0.521	0.521	4.5	14	2355

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	PDB ENTRY 1iw9	2.03	15	23984	18197	18197	88.3	0.207	0.207	0.3586	0.238	0.3435	RANDOM	41.47

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]
-4.469	-5.345		-4.469		8.937

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	17.5706
c_angle_deg	1.17599
c_improper_angle_d	0.76763
c_bond_d	0.006981

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1765
Nucleic Acid Atoms
Solvent Atoms	40
Heterogen Atoms	322

Software

Software
Software Name	Purpose
MAR345dtb	data collection
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
CNS	phasing