2QTZ | pdb_00002qtz

Crystal Structure of the NADP+-bound FAD-containing FNR-like Module of Human Methionine Synthase Reductase

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	277	0.1M Tris HCl, 0.2M KBr, 15% PEG 4000, crystals soaked in saturating levels of NADP+, pH 7.5, vapor diffusion, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.784	α = 90
b = 67.235	β = 106.91
c = 78.615	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	CCD	ADSC QUANTUM 4	monochromator	2005-12-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-3	0.934	ESRF	ID14-3

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	1.9	19.94	98.4	0.052	13		40436	40436

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	1.9	1.97	97.4		0.304			4002

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	1.9	19.94	40156	40156	2014	100	0.17663	0.17663	0.175	0.17	0.211	0.21	RANDOM	29.246

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]
-0.03		-0.03	-0.01		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.006
r_dihedral_angle_4_deg	17.065
r_dihedral_angle_1_deg	13.773
r_dihedral_angle_3_deg	13.709
r_scangle_it	3.806
r_scbond_it	2.406
r_mcangle_it	1.603
r_angle_refined_deg	1.493
r_mcbond_it	1.006
r_nbtor_refined	0.309

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.006
r_dihedral_angle_4_deg	17.065
r_dihedral_angle_1_deg	13.773
r_dihedral_angle_3_deg	13.709
r_scangle_it	3.806
r_scbond_it	2.406
r_mcangle_it	1.603
r_angle_refined_deg	1.493
r_mcbond_it	1.006
r_nbtor_refined	0.309
r_symmetry_vdw_refined	0.204
r_nbd_refined	0.191
r_symmetry_hbond_refined	0.165
r_xyhbond_nbd_refined	0.136
r_chiral_restr	0.106
r_bond_refined_d	0.014
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3494
Nucleic Acid Atoms
Solvent Atoms	352
Heterogen Atoms	74

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.