1QH8 | pdb_00001qh8

NITROGENASE MOFE PROTEIN FROM KLEBSIELLA PNEUMONIAE, AS-CRYSTALLIZED (MIXED OXIDATION) STATE

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8		CRYSTALLIZED ANAEROBICALLY USING LIQUID-LIQUID DIFFUSION TECHNIQUE. FINAL CONCENTRATIONS AFTER EQUILIBRATION WERE: 7% (W/V) PEG 6000, 0.4 - 0.6 M MGCL2, 50 MM TRIS-HCL PH 8, 3.3 MG/ML PROTEIN., pH 8.0, temperature 100K PRIOR TO DATA COLLECTION THE CRYSTAL WAS TRANSIENTLY SOAKED IN CRYOPROTECTANT (MOTHER LIQUOR WITH 25% ETHYLENE GLYCOL) CONTAINING 2 MM SODIUM DITHIONITE (A REDUCTANT).

Crystal Properties
Matthews coefficient	Solvent content
2.31	46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 203.03	α = 90
b = 74.9	β = 122.8
c = 162.12	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	IMAGE PLATE	MARRESEARCH	MIRRORS	1997-07-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11		EMBL/DESY, HAMBURG	X11

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	1.6	50	98	0.044	22.4	3.3		265023		-3	14.83

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)
	1.6	1.63	84.7		0.227	3.82

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1MIN	1.6	50	265023	13327	98	0.155	0.18	0.197	RANDOM	17.71

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]

RMS Deviations
Key	Refinement Restraint Deviation
p_transverse_tor	34.5
p_staggered_tor	13
p_planar_tor	5.2
p_scangle_it	3.773
p_scbond_it	3.056
p_mcangle_it	2.065
p_mcbond_it	1.668
p_multtor_nbd	0.265
p_singtor_nbd	0.171
p_chiral_restr	0.135
p_xyhbond_nbd	0.105
p_planar_d	0.033
p_angle_d	0.028
p_plane_restr	0.0271
p_bond_d	0.013
p_angle_deg
p_hb_or_metal_coord
p_xhyhbond_nbd
p_orthonormal_tor
p_special_tor

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15552
Nucleic Acid Atoms
Solvent Atoms	2809
Heterogen Atoms	204

Software

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