3C78 | pdb_00003c78

0.98 A crystal structure of nitrophorin 4 from Rhodnius prolixus containing FE(III) 2,4 dimethyl deuteroporphyrin ix 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
1.57	20.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.873	α = 90
b = 42.49	β = 94.08
c = 52.633	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 315	BENT CONICAL SI-MIRROR (RH COATING)	2005-02-23	M	SINGLE WAVELENGTH

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

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	0.98	20.28	85.5	0.08	0.08	30.3	4.52		75395			13.4

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)
	0.98	1.02	72		0.4	0.4	4.3	2.04

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	0.98	20.3	75355	3769	85.5	0.167	0.165	0.17	0.189	0.19	RANDOM	13.95

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]
0.02		-0.26	-0.06		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.02
r_dihedral_angle_3_deg	12.115
r_dihedral_angle_1_deg	7.06
r_dihedral_angle_4_deg	6.927
r_sphericity_free	6.482
r_sphericity_bonded	3.857
r_scangle_it	3.637
r_scbond_it	2.931
r_angle_refined_deg	2.446
r_mcangle_it	2.248
r_rigid_bond_restr	2.118
r_mcbond_it	1.573
r_nbd_refined	0.376
r_nbtor_refined	0.312
r_symmetry_vdw_refined	0.179
r_chiral_restr	0.171
r_xyhbond_nbd_refined	0.148
r_symmetry_hbond_refined	0.145
r_metal_ion_refined	0.022
r_bond_refined_d	0.015
r_gen_planes_refined	0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1734
Nucleic Acid Atoms
Solvent Atoms	278
Heterogen Atoms	42

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data scaling