1NVJ | pdb_00001nvj

Deletion Mutant (Delta 141) of Molybdopterin Synthase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1FM0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	295	15% PEG 4000, 10% Isopropanol and 0.1 M Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.128	α = 90
b = 127.832	β = 90
c = 138.118	γ = 90

Symmetry
Space Group	C 2 2 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 QUANTUM 4	Mirrors	2002-08-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	1.1	NSLS	X25

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.15	47.14	92.7	0.063	0.063	17.9	3.3	47232	47232

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.15		73.1		0.367	0.367	1.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	1FM0	2.15	47.14	47231	44837	2394	93.75	0.17901	0.17901	0.17654	0.18	0.22704	0.23	RANDOM	27.949

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]
-0.16			-0.08		0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.256
r_scangle_it	3.242
r_scbond_it	1.897
r_mcangle_it	1.366
r_angle_refined_deg	1.353
r_angle_other_deg	0.83
r_mcbond_it	0.727
r_symmetry_vdw_refined	0.449
r_symmetry_vdw_other	0.295
r_nbd_other	0.243
r_symmetry_hbond_refined	0.242
r_nbd_refined	0.202
r_xyhbond_nbd_refined	0.193
r_chiral_restr	0.085
r_nbtor_other	0.084
r_metal_ion_refined	0.032
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5903
Nucleic Acid Atoms
Solvent Atoms	330
Heterogen Atoms	70

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
ARP/wARP	model building