1SXY | pdb_00001sxy

1.07 A Crystal Structure of D30N Mutant of Nitrophorin 4 from Rhodnius Prolixus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1D2U	PDB entry 1D2U

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	Ammonium Phosphate 3.2 M, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.95	37.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.142	α = 90
b = 42.776	β = 94.05
c = 52.979	γ = 90

Symmetry
Space Group	C 1 2 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	Bent cylindrical Si-mirror (Rh coating)	2002-04-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-D	0.900	APS	14-BM-D

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	1.07	19.83	97.6	0.056	0.056	24.2	5.37	67346	67346			5.48

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)
	1.07	1.11	96.8		0.201	0.201	9.1	5.22	6648

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	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 1D2U	1.07	19.8	67346	63529	3386	96.92	0.15069	0.15069	0.14955	0.16	0.17199	0.16	RANDOM	8.156

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]
-0.19		-0.03	0.1		0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.896
r_sphericity_free	4.895
r_scangle_it	3.562
r_sphericity_bonded	3.381
r_scbond_it	2.501
r_mcangle_it	2.155
r_angle_other_deg	1.927
r_angle_refined_deg	1.759
r_mcbond_it	1.461
r_rigid_bond_restr	1.343
r_symmetry_vdw_other	0.262
r_nbd_other	0.252
r_nbd_refined	0.222
r_symmetry_vdw_refined	0.215
r_xyhbond_nbd_refined	0.176
r_chiral_restr	0.108
r_symmetry_hbond_refined	0.104
r_nbtor_other	0.088
r_metal_ion_refined	0.016
r_bond_refined_d	0.014
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1473
Nucleic Acid Atoms
Solvent Atoms	270
Heterogen Atoms	44

Software

Software
Software Name	Purpose
REFMAC	refinement
XDISPLAYF	data reduction
d*TREK	data scaling