2VRC | pdb_00002vrc

Crystal structure of the Citrobacter sp. triphenylmethane reductase complexed with NADP(H)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8		0.3M NAH2PO4,1.2M KH2PO4,0.2M NACL, 0.1M IMIDAZOLE(PH 8.0)

Crystal Properties
Matthews coefficient	Solvent content
3.17	61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.957	α = 90
b = 76.954	β = 90
c = 272.826	γ = 90

Symmetry
Space Group	P 21 21 21

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	ADSC CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 6C1		PAL/PLS	6C1

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	2.5	30	100	0.05	42.2	6.2		56316		-2

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	2.5	2.59	99.9		0.18	8.45	6

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	NONE	2.5	29.36	51196	2747	100	0.192	0.19	0.1828	0.239	0.2291	RANDOM	41.55

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]
-2.26			4.81		-2.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.389
r_dihedral_angle_3_deg	18.39
r_dihedral_angle_4_deg	18.2
r_dihedral_angle_1_deg	5.756
r_scangle_it	3.325
r_scbond_it	2.245
r_angle_refined_deg	1.391
r_mcangle_it	1.219
r_mcbond_it	1.113
r_nbtor_refined	0.313
r_nbd_refined	0.222
r_symmetry_vdw_refined	0.197
r_symmetry_hbond_refined	0.191
r_xyhbond_nbd_refined	0.143
r_chiral_restr	0.096
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8647
Nucleic Acid Atoms
Solvent Atoms	242
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
SOLVE	phasing