1LS9 | pdb_00001ls9

Structure of the Cytochrome c6 from the Green Alga Cladophora glomerata

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.6	277	0.2 M Na-acetate, 0.1 M Na-cacodylate, pH 6.5, 30% w/v PEG 8000, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.063	α = 90
b = 46.063	β = 90
c = 100.526	γ = 90

Symmetry
Space Group	P 41 21 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	IMAGE PLATE	MARRESEARCH	165-mm MAR CCD	2001-05-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	0.8015	EMBL/DESY, HAMBURG	X13

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.3	14.8906	98.4	0.053	25.3	20.25		27067

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.3	1.32	97.6		0.311	3.6	38.68

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 (All)	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 1CTJ	1.3	14.684	25709	1358	98.6	0.157	0.14922	0.14339	0.148	0.19034	0.1895	RANDOM	16.595

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]
0.4835			0.4835		0.0177

RMS Deviations
Key	Refinement Restraint Deviation
p_transverse_tor	17.8
p_staggered_tor	11.2
p_planar_tor	5.3
p_scangle_it	4.29
p_scbond_it	3.384
p_mcangle_it	2.8
p_mcbond_it	2.405
p_multtor_nbd	0.278
p_singtor_nbd	0.165
p_chiral_restr	0.138
p_xyhbond_nbd	0.071
p_hb_or_metal_coord	0.059
p_planar_d	0.035
p_angle_d	0.033
p_bond_d	0.024
p_plane_restr	0.016
o_bond_d_na
o_bond_d_prot
p_xhyhbond_nbd
p_special_tor

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	674
Nucleic Acid Atoms
Solvent Atoms	200
Heterogen Atoms	43

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement