2YL0

CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: AS ISOLATED L16A VARIANT AT 0.95 A RESOLUTION

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		AMMONIUM SULPHATE, TRIS PH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.4	α = 90
b = 53.4	β = 90
c = 181.25	γ = 120

Symmetry
Space Group	P 65 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	PIXEL	DECTRIS PILATUS 6M	MIRRORS	2008-04-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0,8	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	0.93	46	99.8	0.06	13.6	6		103306			11.8

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	0.93	1	99.9		0.99	1.9	5.7

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2YKZ	0.95	46.22	92749	3865	100	0.13284	0.13213	0.14968	RANDOM	13.811

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]
-0.69	-0.34		-0.69		1.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.898
r_dihedral_angle_3_deg	13.584
r_dihedral_angle_4_deg	13.189
r_dihedral_angle_1_deg	5.269
r_scangle_it	3.71
r_scbond_it	2.721
r_mcangle_it	2.108
r_angle_refined_deg	1.813
r_mcbond_it	1.378
r_rigid_bond_restr	1.206
r_angle_other_deg	0.991
r_mcbond_other	0.513
r_chiral_restr	0.109
r_bond_refined_d	0.017
r_gen_planes_refined	0.012
r_gen_planes_other	0.005
r_bond_other_d	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	955
Nucleic Acid Atoms
Solvent Atoms	354
Heterogen Atoms	45

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing