2VMJ | pdb_00002vmj

Type 1 Copper-Binding Loop of Nitrite Reductase mutant: 130- CAPEGMVPWHVVSGM-144 to 130-CTPHPFM-136

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OE1	PDB ENTRY 1OE1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		50 MM HEPES PH 7.0, 5 MM ZNCL2 AND 10 % PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
3.01	59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.813	α = 90
b = 89.813	β = 90
c = 143.099	γ = 120

Symmetry
Space Group	H 3

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	MARRESEARCH			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX10.1		SRS	PX10.1

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	37.5	98.4	0.06	9.4	1.8		14625

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	2.56	99.9		0.19	2.4	1.8

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1OE1	2.5	37.53	13879	746	98.3	0.184	0.181	0.18	0.232	0.23	RANDOM	54.2

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]
-0.01	-0.01		-0.01		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.444
r_dihedral_angle_4_deg	20.521
r_dihedral_angle_3_deg	15.737
r_dihedral_angle_1_deg	7
r_scangle_it	2.366
r_scbond_it	1.553
r_angle_refined_deg	1.536
r_mcangle_it	1.192
r_mcbond_it	0.708
r_nbtor_refined	0.309
r_nbd_refined	0.212
r_xyhbond_nbd_refined	0.154
r_symmetry_vdw_refined	0.15
r_symmetry_hbond_refined	0.15
r_chiral_restr	0.102
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
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	2469
Nucleic Acid Atoms
Solvent Atoms	90
Heterogen Atoms	18

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing