3C76 | pdb_00003c76

1.07 A crystal structure of L133V mutant of nitrophorin 4 from Rhodnius prolixus complexed with ammonia at PH 7.5

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1X8P	PDB ENTRY 1X8P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	300	AMMONIUM PHOSPHATE, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 300.0K

Crystal Properties
Matthews coefficient	Solvent content
1.62	23.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.32	α = 90
b = 42.847	β = 94.26
c = 52.871	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-FLAT 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		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	19.85	97.5	0.06	0.06	15.4	7.12		67479			10.9

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	98		0.3	0.3	4	6.79

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	FOURIER SYNTHESIS	FREE R	PDB ENTRY 1X8P	1.07	19.8	67317	3416	97.3	0.141	0.139	0.15	0.165	0.17	RANDOM	8.69

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]
0.07		-0.02	-0.12		0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.505
r_dihedral_angle_3_deg	12.807
r_dihedral_angle_4_deg	8.491
r_dihedral_angle_1_deg	7.791
r_sphericity_free	7.658
r_scangle_it	3.716
r_sphericity_bonded	3.229
r_scbond_it	3.073
r_mcangle_it	2.235
r_mcbond_it	1.836
r_angle_refined_deg	1.743
r_rigid_bond_restr	1.467
r_angle_other_deg	0.889
r_mcbond_other	0.685
r_nbd_refined	0.417
r_nbd_other	0.22
r_symmetry_vdw_other	0.189
r_nbtor_refined	0.187
r_xyhbond_nbd_refined	0.16
r_chiral_restr	0.101
r_symmetry_hbond_refined	0.1
r_nbtor_other	0.091
r_symmetry_vdw_refined	0.085
r_xyhbond_nbd_other	0.049
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_gen_planes_other	0.004
r_bond_other_d	0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1712
Nucleic Acid Atoms
Solvent Atoms	304
Heterogen Atoms	44

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data scaling
d*TREK	data scaling