8AEP | pdb_00008aep

Reductase domain of the carboxylate reductase of Neurospora crassa

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5MSP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		289.15	Crystals were grown by mixing 0.5 microL 0.2 M ammonia sulphate, 0.1 M BisTRIS pH 5.5 and 25 percent PEG 3350 with 0.5 microL 18.00 mg per mL NcCAR R-domain in 50 mM MES buffer pH pH 7.0 containing 10 mM magnesium chloride, 150 mM sodium chloride and 1 mM DTT. Crystals appeared after 6-9 weeks under vapor batch conditions.

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.235	α = 90
b = 137.487	β = 112.333
c = 66.513	γ = 90

Symmetry
Space Group	P 1 21 1

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 2M		2018-10-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.87313	ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.3	48.651	99.7	0.191	0.257	0.171	0.98	5.8	3.8		41333

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.38			0.704	0.949	0.631	0.636		3.9

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5MSP	2.3	48.651	41299	2039	99.614	0.203	0.2002	0.21	0.2586	0.26	26.121

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]
0.551		-1.231	0.075		0.288

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.216
r_dihedral_angle_4_deg	19.938
r_dihedral_angle_3_deg	12.175
r_dihedral_angle_1_deg	7.018
r_lrange_it	6.997
r_lrange_other	6.862
r_scangle_it	4.608
r_scangle_other	4.603
r_mcangle_it	3.915
r_mcangle_other	3.915
r_scbond_it	2.769
r_scbond_other	2.764
r_mcbond_it	2.428
r_mcbond_other	2.427
r_angle_refined_deg	1.486
r_angle_other_deg	1.267
r_symmetry_xyhbond_nbd_refined	0.327
r_nbd_other	0.246
r_symmetry_nbd_refined	0.196
r_nbd_refined	0.193
r_symmetry_nbd_other	0.178
r_xyhbond_nbd_refined	0.178
r_nbtor_refined	0.156
r_symmetry_xyhbond_nbd_other	0.153
r_ncsr_local_group_1	0.085
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.068
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6206
Nucleic Acid Atoms
Solvent Atoms	741
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
MOLREP	phasing
Coot	model building